├── .gitignore
├── LICENSE
├── MANIFEST.in
├── Makefile
├── README.rst
├── cdindex
├── __init__.py
├── cdindex.py
├── pycdindex.c
└── time_utilities.py
├── docs
├── Makefile
├── cdindex.cdindex.rst
├── cdindex.rst
├── cdindex.time_utilities.rst
├── conf.py
├── index.rst
└── modules.rst
├── setup.py
├── src
├── cdindex.c
├── cdindex.h
├── graph.c
├── main.c
└── utility.c
└── tests.py
/.gitignore:
--------------------------------------------------------------------------------
1 | # Byte-compiled / optimized / DLL files
2 | __pycache__/
3 | *.py[cod]
4 | *$py.class
5 |
6 | # C extensions
7 | *.so
8 |
9 | # Distribution / packaging
10 | .Python
11 | env/
12 | build/
13 | develop-eggs/
14 | dist/
15 | downloads/
16 | eggs/
17 | .eggs/
18 | lib/
19 | lib64/
20 | parts/
21 | sdist/
22 | var/
23 | wheels/
24 | *.egg-info/
25 | .installed.cfg
26 | *.egg
27 |
28 | # PyInstaller
29 | # Usually these files are written by a python script from a template
30 | # before PyInstaller builds the exe, so as to inject date/other infos into it.
31 | *.manifest
32 | *.spec
33 |
34 | # Installer logs
35 | pip-log.txt
36 | pip-delete-this-directory.txt
37 |
38 | # Unit test / coverage reports
39 | htmlcov/
40 | .tox/
41 | .coverage
42 | .coverage.*
43 | .cache
44 | nosetests.xml
45 | coverage.xml
46 | *.cover
47 | .hypothesis/
48 |
49 | # Translations
50 | *.mo
51 | *.pot
52 |
53 | # Django stuff:
54 | *.log
55 | local_settings.py
56 |
57 | # Flask stuff:
58 | instance/
59 | .webassets-cache
60 |
61 | # Scrapy stuff:
62 | .scrapy
63 |
64 | # Sphinx documentation
65 | docs/_build/
66 |
67 | # PyBuilder
68 | target/
69 |
70 | # Jupyter Notebook
71 | .ipynb_checkpoints
72 |
73 | # pyenv
74 | .python-version
75 |
76 | # celery beat schedule file
77 | celerybeat-schedule
78 |
79 | # SageMath parsed files
80 | *.sage.py
81 |
82 | # dotenv
83 | .env
84 |
85 | # virtualenv
86 | .venv
87 | venv/
88 | ENV/
89 |
90 | # Spyder project settings
91 | .spyderproject
92 | .spyproject
93 |
94 | # Rope project settings
95 | .ropeproject
96 |
97 | # mkdocs documentation
98 | /site
99 |
100 | # mypy
101 | .mypy_cache/
102 |
103 | # os x
104 | .DS_Store
--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
1 | GNU GENERAL PUBLIC LICENSE
2 | Version 3, 29 June 2007
3 |
4 | Copyright (C) 2007 Free Software Foundation, Inc.
5 | Everyone is permitted to copy and distribute verbatim copies
6 | of this license document, but changing it is not allowed.
7 |
8 | Preamble
9 |
10 | The GNU General Public License is a free, copyleft license for
11 | software and other kinds of works.
12 |
13 | The licenses for most software and other practical works are designed
14 | to take away your freedom to share and change the works. By contrast,
15 | the GNU General Public License is intended to guarantee your freedom to
16 | share and change all versions of a program--to make sure it remains free
17 | software for all its users. We, the Free Software Foundation, use the
18 | GNU General Public License for most of our software; it applies also to
19 | any other work released this way by its authors. You can apply it to
20 | your programs, too.
21 |
22 | When we speak of free software, we are referring to freedom, not
23 | price. Our General Public Licenses are designed to make sure that you
24 | have the freedom to distribute copies of free software (and charge for
25 | them if you wish), that you receive source code or can get it if you
26 | want it, that you can change the software or use pieces of it in new
27 | free programs, and that you know you can do these things.
28 |
29 | To protect your rights, we need to prevent others from denying you
30 | these rights or asking you to surrender the rights. Therefore, you have
31 | certain responsibilities if you distribute copies of the software, or if
32 | you modify it: responsibilities to respect the freedom of others.
33 |
34 | For example, if you distribute copies of such a program, whether
35 | gratis or for a fee, you must pass on to the recipients the same
36 | freedoms that you received. You must make sure that they, too, receive
37 | or can get the source code. And you must show them these terms so they
38 | know their rights.
39 |
40 | Developers that use the GNU GPL protect your rights with two steps:
41 | (1) assert copyright on the software, and (2) offer you this License
42 | giving you legal permission to copy, distribute and/or modify it.
43 |
44 | For the developers' and authors' protection, the GPL clearly explains
45 | that there is no warranty for this free software. For both users' and
46 | authors' sake, the GPL requires that modified versions be marked as
47 | changed, so that their problems will not be attributed erroneously to
48 | authors of previous versions.
49 |
50 | Some devices are designed to deny users access to install or run
51 | modified versions of the software inside them, although the manufacturer
52 | can do so. This is fundamentally incompatible with the aim of
53 | protecting users' freedom to change the software. The systematic
54 | pattern of such abuse occurs in the area of products for individuals to
55 | use, which is precisely where it is most unacceptable. Therefore, we
56 | have designed this version of the GPL to prohibit the practice for those
57 | products. If such problems arise substantially in other domains, we
58 | stand ready to extend this provision to those domains in future versions
59 | of the GPL, as needed to protect the freedom of users.
60 |
61 | Finally, every program is threatened constantly by software patents.
62 | States should not allow patents to restrict development and use of
63 | software on general-purpose computers, but in those that do, we wish to
64 | avoid the special danger that patents applied to a free program could
65 | make it effectively proprietary. To prevent this, the GPL assures that
66 | patents cannot be used to render the program non-free.
67 |
68 | The precise terms and conditions for copying, distribution and
69 | modification follow.
70 |
71 | TERMS AND CONDITIONS
72 |
73 | 0. Definitions.
74 |
75 | "This License" refers to version 3 of the GNU General Public License.
76 |
77 | "Copyright" also means copyright-like laws that apply to other kinds of
78 | works, such as semiconductor masks.
79 |
80 | "The Program" refers to any copyrightable work licensed under this
81 | License. Each licensee is addressed as "you". "Licensees" and
82 | "recipients" may be individuals or organizations.
83 |
84 | To "modify" a work means to copy from or adapt all or part of the work
85 | in a fashion requiring copyright permission, other than the making of an
86 | exact copy. The resulting work is called a "modified version" of the
87 | earlier work or a work "based on" the earlier work.
88 |
89 | A "covered work" means either the unmodified Program or a work based
90 | on the Program.
91 |
92 | To "propagate" a work means to do anything with it that, without
93 | permission, would make you directly or secondarily liable for
94 | infringement under applicable copyright law, except executing it on a
95 | computer or modifying a private copy. Propagation includes copying,
96 | distribution (with or without modification), making available to the
97 | public, and in some countries other activities as well.
98 |
99 | To "convey" a work means any kind of propagation that enables other
100 | parties to make or receive copies. Mere interaction with a user through
101 | a computer network, with no transfer of a copy, is not conveying.
102 |
103 | An interactive user interface displays "Appropriate Legal Notices"
104 | to the extent that it includes a convenient and prominently visible
105 | feature that (1) displays an appropriate copyright notice, and (2)
106 | tells the user that there is no warranty for the work (except to the
107 | extent that warranties are provided), that licensees may convey the
108 | work under this License, and how to view a copy of this License. If
109 | the interface presents a list of user commands or options, such as a
110 | menu, a prominent item in the list meets this criterion.
111 |
112 | 1. Source Code.
113 |
114 | The "source code" for a work means the preferred form of the work
115 | for making modifications to it. "Object code" means any non-source
116 | form of a work.
117 |
118 | A "Standard Interface" means an interface that either is an official
119 | standard defined by a recognized standards body, or, in the case of
120 | interfaces specified for a particular programming language, one that
121 | is widely used among developers working in that language.
122 |
123 | The "System Libraries" of an executable work include anything, other
124 | than the work as a whole, that (a) is included in the normal form of
125 | packaging a Major Component, but which is not part of that Major
126 | Component, and (b) serves only to enable use of the work with that
127 | Major Component, or to implement a Standard Interface for which an
128 | implementation is available to the public in source code form. A
129 | "Major Component", in this context, means a major essential component
130 | (kernel, window system, and so on) of the specific operating system
131 | (if any) on which the executable work runs, or a compiler used to
132 | produce the work, or an object code interpreter used to run it.
133 |
134 | The "Corresponding Source" for a work in object code form means all
135 | the source code needed to generate, install, and (for an executable
136 | work) run the object code and to modify the work, including scripts to
137 | control those activities. However, it does not include the work's
138 | System Libraries, or general-purpose tools or generally available free
139 | programs which are used unmodified in performing those activities but
140 | which are not part of the work. For example, Corresponding Source
141 | includes interface definition files associated with source files for
142 | the work, and the source code for shared libraries and dynamically
143 | linked subprograms that the work is specifically designed to require,
144 | such as by intimate data communication or control flow between those
145 | subprograms and other parts of the work.
146 |
147 | The Corresponding Source need not include anything that users
148 | can regenerate automatically from other parts of the Corresponding
149 | Source.
150 |
151 | The Corresponding Source for a work in source code form is that
152 | same work.
153 |
154 | 2. Basic Permissions.
155 |
156 | All rights granted under this License are granted for the term of
157 | copyright on the Program, and are irrevocable provided the stated
158 | conditions are met. This License explicitly affirms your unlimited
159 | permission to run the unmodified Program. The output from running a
160 | covered work is covered by this License only if the output, given its
161 | content, constitutes a covered work. This License acknowledges your
162 | rights of fair use or other equivalent, as provided by copyright law.
163 |
164 | You may make, run and propagate covered works that you do not
165 | convey, without conditions so long as your license otherwise remains
166 | in force. You may convey covered works to others for the sole purpose
167 | of having them make modifications exclusively for you, or provide you
168 | with facilities for running those works, provided that you comply with
169 | the terms of this License in conveying all material for which you do
170 | not control copyright. Those thus making or running the covered works
171 | for you must do so exclusively on your behalf, under your direction
172 | and control, on terms that prohibit them from making any copies of
173 | your copyrighted material outside their relationship with you.
174 |
175 | Conveying under any other circumstances is permitted solely under
176 | the conditions stated below. Sublicensing is not allowed; section 10
177 | makes it unnecessary.
178 |
179 | 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
180 |
181 | No covered work shall be deemed part of an effective technological
182 | measure under any applicable law fulfilling obligations under article
183 | 11 of the WIPO copyright treaty adopted on 20 December 1996, or
184 | similar laws prohibiting or restricting circumvention of such
185 | measures.
186 |
187 | When you convey a covered work, you waive any legal power to forbid
188 | circumvention of technological measures to the extent such circumvention
189 | is effected by exercising rights under this License with respect to
190 | the covered work, and you disclaim any intention to limit operation or
191 | modification of the work as a means of enforcing, against the work's
192 | users, your or third parties' legal rights to forbid circumvention of
193 | technological measures.
194 |
195 | 4. Conveying Verbatim Copies.
196 |
197 | You may convey verbatim copies of the Program's source code as you
198 | receive it, in any medium, provided that you conspicuously and
199 | appropriately publish on each copy an appropriate copyright notice;
200 | keep intact all notices stating that this License and any
201 | non-permissive terms added in accord with section 7 apply to the code;
202 | keep intact all notices of the absence of any warranty; and give all
203 | recipients a copy of this License along with the Program.
204 |
205 | You may charge any price or no price for each copy that you convey,
206 | and you may offer support or warranty protection for a fee.
207 |
208 | 5. Conveying Modified Source Versions.
209 |
210 | You may convey a work based on the Program, or the modifications to
211 | produce it from the Program, in the form of source code under the
212 | terms of section 4, provided that you also meet all of these conditions:
213 |
214 | a) The work must carry prominent notices stating that you modified
215 | it, and giving a relevant date.
216 |
217 | b) The work must carry prominent notices stating that it is
218 | released under this License and any conditions added under section
219 | 7. This requirement modifies the requirement in section 4 to
220 | "keep intact all notices".
221 |
222 | c) You must license the entire work, as a whole, under this
223 | License to anyone who comes into possession of a copy. This
224 | License will therefore apply, along with any applicable section 7
225 | additional terms, to the whole of the work, and all its parts,
226 | regardless of how they are packaged. This License gives no
227 | permission to license the work in any other way, but it does not
228 | invalidate such permission if you have separately received it.
229 |
230 | d) If the work has interactive user interfaces, each must display
231 | Appropriate Legal Notices; however, if the Program has interactive
232 | interfaces that do not display Appropriate Legal Notices, your
233 | work need not make them do so.
234 |
235 | A compilation of a covered work with other separate and independent
236 | works, which are not by their nature extensions of the covered work,
237 | and which are not combined with it such as to form a larger program,
238 | in or on a volume of a storage or distribution medium, is called an
239 | "aggregate" if the compilation and its resulting copyright are not
240 | used to limit the access or legal rights of the compilation's users
241 | beyond what the individual works permit. Inclusion of a covered work
242 | in an aggregate does not cause this License to apply to the other
243 | parts of the aggregate.
244 |
245 | 6. Conveying Non-Source Forms.
246 |
247 | You may convey a covered work in object code form under the terms
248 | of sections 4 and 5, provided that you also convey the
249 | machine-readable Corresponding Source under the terms of this License,
250 | in one of these ways:
251 |
252 | a) Convey the object code in, or embodied in, a physical product
253 | (including a physical distribution medium), accompanied by the
254 | Corresponding Source fixed on a durable physical medium
255 | customarily used for software interchange.
256 |
257 | b) Convey the object code in, or embodied in, a physical product
258 | (including a physical distribution medium), accompanied by a
259 | written offer, valid for at least three years and valid for as
260 | long as you offer spare parts or customer support for that product
261 | model, to give anyone who possesses the object code either (1) a
262 | copy of the Corresponding Source for all the software in the
263 | product that is covered by this License, on a durable physical
264 | medium customarily used for software interchange, for a price no
265 | more than your reasonable cost of physically performing this
266 | conveying of source, or (2) access to copy the
267 | Corresponding Source from a network server at no charge.
268 |
269 | c) Convey individual copies of the object code with a copy of the
270 | written offer to provide the Corresponding Source. This
271 | alternative is allowed only occasionally and noncommercially, and
272 | only if you received the object code with such an offer, in accord
273 | with subsection 6b.
274 |
275 | d) Convey the object code by offering access from a designated
276 | place (gratis or for a charge), and offer equivalent access to the
277 | Corresponding Source in the same way through the same place at no
278 | further charge. You need not require recipients to copy the
279 | Corresponding Source along with the object code. If the place to
280 | copy the object code is a network server, the Corresponding Source
281 | may be on a different server (operated by you or a third party)
282 | that supports equivalent copying facilities, provided you maintain
283 | clear directions next to the object code saying where to find the
284 | Corresponding Source. Regardless of what server hosts the
285 | Corresponding Source, you remain obligated to ensure that it is
286 | available for as long as needed to satisfy these requirements.
287 |
288 | e) Convey the object code using peer-to-peer transmission, provided
289 | you inform other peers where the object code and Corresponding
290 | Source of the work are being offered to the general public at no
291 | charge under subsection 6d.
292 |
293 | A separable portion of the object code, whose source code is excluded
294 | from the Corresponding Source as a System Library, need not be
295 | included in conveying the object code work.
296 |
297 | A "User Product" is either (1) a "consumer product", which means any
298 | tangible personal property which is normally used for personal, family,
299 | or household purposes, or (2) anything designed or sold for incorporation
300 | into a dwelling. In determining whether a product is a consumer product,
301 | doubtful cases shall be resolved in favor of coverage. For a particular
302 | product received by a particular user, "normally used" refers to a
303 | typical or common use of that class of product, regardless of the status
304 | of the particular user or of the way in which the particular user
305 | actually uses, or expects or is expected to use, the product. A product
306 | is a consumer product regardless of whether the product has substantial
307 | commercial, industrial or non-consumer uses, unless such uses represent
308 | the only significant mode of use of the product.
309 |
310 | "Installation Information" for a User Product means any methods,
311 | procedures, authorization keys, or other information required to install
312 | and execute modified versions of a covered work in that User Product from
313 | a modified version of its Corresponding Source. The information must
314 | suffice to ensure that the continued functioning of the modified object
315 | code is in no case prevented or interfered with solely because
316 | modification has been made.
317 |
318 | If you convey an object code work under this section in, or with, or
319 | specifically for use in, a User Product, and the conveying occurs as
320 | part of a transaction in which the right of possession and use of the
321 | User Product is transferred to the recipient in perpetuity or for a
322 | fixed term (regardless of how the transaction is characterized), the
323 | Corresponding Source conveyed under this section must be accompanied
324 | by the Installation Information. But this requirement does not apply
325 | if neither you nor any third party retains the ability to install
326 | modified object code on the User Product (for example, the work has
327 | been installed in ROM).
328 |
329 | The requirement to provide Installation Information does not include a
330 | requirement to continue to provide support service, warranty, or updates
331 | for a work that has been modified or installed by the recipient, or for
332 | the User Product in which it has been modified or installed. Access to a
333 | network may be denied when the modification itself materially and
334 | adversely affects the operation of the network or violates the rules and
335 | protocols for communication across the network.
336 |
337 | Corresponding Source conveyed, and Installation Information provided,
338 | in accord with this section must be in a format that is publicly
339 | documented (and with an implementation available to the public in
340 | source code form), and must require no special password or key for
341 | unpacking, reading or copying.
342 |
343 | 7. Additional Terms.
344 |
345 | "Additional permissions" are terms that supplement the terms of this
346 | License by making exceptions from one or more of its conditions.
347 | Additional permissions that are applicable to the entire Program shall
348 | be treated as though they were included in this License, to the extent
349 | that they are valid under applicable law. If additional permissions
350 | apply only to part of the Program, that part may be used separately
351 | under those permissions, but the entire Program remains governed by
352 | this License without regard to the additional permissions.
353 |
354 | When you convey a copy of a covered work, you may at your option
355 | remove any additional permissions from that copy, or from any part of
356 | it. (Additional permissions may be written to require their own
357 | removal in certain cases when you modify the work.) You may place
358 | additional permissions on material, added by you to a covered work,
359 | for which you have or can give appropriate copyright permission.
360 |
361 | Notwithstanding any other provision of this License, for material you
362 | add to a covered work, you may (if authorized by the copyright holders of
363 | that material) supplement the terms of this License with terms:
364 |
365 | a) Disclaiming warranty or limiting liability differently from the
366 | terms of sections 15 and 16 of this License; or
367 |
368 | b) Requiring preservation of specified reasonable legal notices or
369 | author attributions in that material or in the Appropriate Legal
370 | Notices displayed by works containing it; or
371 |
372 | c) Prohibiting misrepresentation of the origin of that material, or
373 | requiring that modified versions of such material be marked in
374 | reasonable ways as different from the original version; or
375 |
376 | d) Limiting the use for publicity purposes of names of licensors or
377 | authors of the material; or
378 |
379 | e) Declining to grant rights under trademark law for use of some
380 | trade names, trademarks, or service marks; or
381 |
382 | f) Requiring indemnification of licensors and authors of that
383 | material by anyone who conveys the material (or modified versions of
384 | it) with contractual assumptions of liability to the recipient, for
385 | any liability that these contractual assumptions directly impose on
386 | those licensors and authors.
387 |
388 | All other non-permissive additional terms are considered "further
389 | restrictions" within the meaning of section 10. If the Program as you
390 | received it, or any part of it, contains a notice stating that it is
391 | governed by this License along with a term that is a further
392 | restriction, you may remove that term. If a license document contains
393 | a further restriction but permits relicensing or conveying under this
394 | License, you may add to a covered work material governed by the terms
395 | of that license document, provided that the further restriction does
396 | not survive such relicensing or conveying.
397 |
398 | If you add terms to a covered work in accord with this section, you
399 | must place, in the relevant source files, a statement of the
400 | additional terms that apply to those files, or a notice indicating
401 | where to find the applicable terms.
402 |
403 | Additional terms, permissive or non-permissive, may be stated in the
404 | form of a separately written license, or stated as exceptions;
405 | the above requirements apply either way.
406 |
407 | 8. Termination.
408 |
409 | You may not propagate or modify a covered work except as expressly
410 | provided under this License. Any attempt otherwise to propagate or
411 | modify it is void, and will automatically terminate your rights under
412 | this License (including any patent licenses granted under the third
413 | paragraph of section 11).
414 |
415 | However, if you cease all violation of this License, then your
416 | license from a particular copyright holder is reinstated (a)
417 | provisionally, unless and until the copyright holder explicitly and
418 | finally terminates your license, and (b) permanently, if the copyright
419 | holder fails to notify you of the violation by some reasonable means
420 | prior to 60 days after the cessation.
421 |
422 | Moreover, your license from a particular copyright holder is
423 | reinstated permanently if the copyright holder notifies you of the
424 | violation by some reasonable means, this is the first time you have
425 | received notice of violation of this License (for any work) from that
426 | copyright holder, and you cure the violation prior to 30 days after
427 | your receipt of the notice.
428 |
429 | Termination of your rights under this section does not terminate the
430 | licenses of parties who have received copies or rights from you under
431 | this License. If your rights have been terminated and not permanently
432 | reinstated, you do not qualify to receive new licenses for the same
433 | material under section 10.
434 |
435 | 9. Acceptance Not Required for Having Copies.
436 |
437 | You are not required to accept this License in order to receive or
438 | run a copy of the Program. Ancillary propagation of a covered work
439 | occurring solely as a consequence of using peer-to-peer transmission
440 | to receive a copy likewise does not require acceptance. However,
441 | nothing other than this License grants you permission to propagate or
442 | modify any covered work. These actions infringe copyright if you do
443 | not accept this License. Therefore, by modifying or propagating a
444 | covered work, you indicate your acceptance of this License to do so.
445 |
446 | 10. Automatic Licensing of Downstream Recipients.
447 |
448 | Each time you convey a covered work, the recipient automatically
449 | receives a license from the original licensors, to run, modify and
450 | propagate that work, subject to this License. You are not responsible
451 | for enforcing compliance by third parties with this License.
452 |
453 | An "entity transaction" is a transaction transferring control of an
454 | organization, or substantially all assets of one, or subdividing an
455 | organization, or merging organizations. If propagation of a covered
456 | work results from an entity transaction, each party to that
457 | transaction who receives a copy of the work also receives whatever
458 | licenses to the work the party's predecessor in interest had or could
459 | give under the previous paragraph, plus a right to possession of the
460 | Corresponding Source of the work from the predecessor in interest, if
461 | the predecessor has it or can get it with reasonable efforts.
462 |
463 | You may not impose any further restrictions on the exercise of the
464 | rights granted or affirmed under this License. For example, you may
465 | not impose a license fee, royalty, or other charge for exercise of
466 | rights granted under this License, and you may not initiate litigation
467 | (including a cross-claim or counterclaim in a lawsuit) alleging that
468 | any patent claim is infringed by making, using, selling, offering for
469 | sale, or importing the Program or any portion of it.
470 |
471 | 11. Patents.
472 |
473 | A "contributor" is a copyright holder who authorizes use under this
474 | License of the Program or a work on which the Program is based. The
475 | work thus licensed is called the contributor's "contributor version".
476 |
477 | A contributor's "essential patent claims" are all patent claims
478 | owned or controlled by the contributor, whether already acquired or
479 | hereafter acquired, that would be infringed by some manner, permitted
480 | by this License, of making, using, or selling its contributor version,
481 | but do not include claims that would be infringed only as a
482 | consequence of further modification of the contributor version. For
483 | purposes of this definition, "control" includes the right to grant
484 | patent sublicenses in a manner consistent with the requirements of
485 | this License.
486 |
487 | Each contributor grants you a non-exclusive, worldwide, royalty-free
488 | patent license under the contributor's essential patent claims, to
489 | make, use, sell, offer for sale, import and otherwise run, modify and
490 | propagate the contents of its contributor version.
491 |
492 | In the following three paragraphs, a "patent license" is any express
493 | agreement or commitment, however denominated, not to enforce a patent
494 | (such as an express permission to practice a patent or covenant not to
495 | sue for patent infringement). To "grant" such a patent license to a
496 | party means to make such an agreement or commitment not to enforce a
497 | patent against the party.
498 |
499 | If you convey a covered work, knowingly relying on a patent license,
500 | and the Corresponding Source of the work is not available for anyone
501 | to copy, free of charge and under the terms of this License, through a
502 | publicly available network server or other readily accessible means,
503 | then you must either (1) cause the Corresponding Source to be so
504 | available, or (2) arrange to deprive yourself of the benefit of the
505 | patent license for this particular work, or (3) arrange, in a manner
506 | consistent with the requirements of this License, to extend the patent
507 | license to downstream recipients. "Knowingly relying" means you have
508 | actual knowledge that, but for the patent license, your conveying the
509 | covered work in a country, or your recipient's use of the covered work
510 | in a country, would infringe one or more identifiable patents in that
511 | country that you have reason to believe are valid.
512 |
513 | If, pursuant to or in connection with a single transaction or
514 | arrangement, you convey, or propagate by procuring conveyance of, a
515 | covered work, and grant a patent license to some of the parties
516 | receiving the covered work authorizing them to use, propagate, modify
517 | or convey a specific copy of the covered work, then the patent license
518 | you grant is automatically extended to all recipients of the covered
519 | work and works based on it.
520 |
521 | A patent license is "discriminatory" if it does not include within
522 | the scope of its coverage, prohibits the exercise of, or is
523 | conditioned on the non-exercise of one or more of the rights that are
524 | specifically granted under this License. You may not convey a covered
525 | work if you are a party to an arrangement with a third party that is
526 | in the business of distributing software, under which you make payment
527 | to the third party based on the extent of your activity of conveying
528 | the work, and under which the third party grants, to any of the
529 | parties who would receive the covered work from you, a discriminatory
530 | patent license (a) in connection with copies of the covered work
531 | conveyed by you (or copies made from those copies), or (b) primarily
532 | for and in connection with specific products or compilations that
533 | contain the covered work, unless you entered into that arrangement,
534 | or that patent license was granted, prior to 28 March 2007.
535 |
536 | Nothing in this License shall be construed as excluding or limiting
537 | any implied license or other defenses to infringement that may
538 | otherwise be available to you under applicable patent law.
539 |
540 | 12. No Surrender of Others' Freedom.
541 |
542 | If conditions are imposed on you (whether by court order, agreement or
543 | otherwise) that contradict the conditions of this License, they do not
544 | excuse you from the conditions of this License. If you cannot convey a
545 | covered work so as to satisfy simultaneously your obligations under this
546 | License and any other pertinent obligations, then as a consequence you may
547 | not convey it at all. For example, if you agree to terms that obligate you
548 | to collect a royalty for further conveying from those to whom you convey
549 | the Program, the only way you could satisfy both those terms and this
550 | License would be to refrain entirely from conveying the Program.
551 |
552 | 13. Use with the GNU Affero General Public License.
553 |
554 | Notwithstanding any other provision of this License, you have
555 | permission to link or combine any covered work with a work licensed
556 | under version 3 of the GNU Affero General Public License into a single
557 | combined work, and to convey the resulting work. The terms of this
558 | License will continue to apply to the part which is the covered work,
559 | but the special requirements of the GNU Affero General Public License,
560 | section 13, concerning interaction through a network will apply to the
561 | combination as such.
562 |
563 | 14. Revised Versions of this License.
564 |
565 | The Free Software Foundation may publish revised and/or new versions of
566 | the GNU General Public License from time to time. Such new versions will
567 | be similar in spirit to the present version, but may differ in detail to
568 | address new problems or concerns.
569 |
570 | Each version is given a distinguishing version number. If the
571 | Program specifies that a certain numbered version of the GNU General
572 | Public License "or any later version" applies to it, you have the
573 | option of following the terms and conditions either of that numbered
574 | version or of any later version published by the Free Software
575 | Foundation. If the Program does not specify a version number of the
576 | GNU General Public License, you may choose any version ever published
577 | by the Free Software Foundation.
578 |
579 | If the Program specifies that a proxy can decide which future
580 | versions of the GNU General Public License can be used, that proxy's
581 | public statement of acceptance of a version permanently authorizes you
582 | to choose that version for the Program.
583 |
584 | Later license versions may give you additional or different
585 | permissions. However, no additional obligations are imposed on any
586 | author or copyright holder as a result of your choosing to follow a
587 | later version.
588 |
589 | 15. Disclaimer of Warranty.
590 |
591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
599 |
600 | 16. Limitation of Liability.
601 |
602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
610 | SUCH DAMAGES.
611 |
612 | 17. Interpretation of Sections 15 and 16.
613 |
614 | If the disclaimer of warranty and limitation of liability provided
615 | above cannot be given local legal effect according to their terms,
616 | reviewing courts shall apply local law that most closely approximates
617 | an absolute waiver of all civil liability in connection with the
618 | Program, unless a warranty or assumption of liability accompanies a
619 | copy of the Program in return for a fee.
620 |
621 | END OF TERMS AND CONDITIONS
622 |
623 | How to Apply These Terms to Your New Programs
624 |
625 | If you develop a new program, and you want it to be of the greatest
626 | possible use to the public, the best way to achieve this is to make it
627 | free software which everyone can redistribute and change under these terms.
628 |
629 | To do so, attach the following notices to the program. It is safest
630 | to attach them to the start of each source file to most effectively
631 | state the exclusion of warranty; and each file should have at least
632 | the "copyright" line and a pointer to where the full notice is found.
633 |
634 | {one line to give the program's name and a brief idea of what it does.}
635 | Copyright (C) {year} {name of author}
636 |
637 | This program is free software: you can redistribute it and/or modify
638 | it under the terms of the GNU General Public License as published by
639 | the Free Software Foundation, either version 3 of the License, or
640 | (at your option) any later version.
641 |
642 | This program is distributed in the hope that it will be useful,
643 | but WITHOUT ANY WARRANTY; without even the implied warranty of
644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
645 | GNU General Public License for more details.
646 |
647 | You should have received a copy of the GNU General Public License
648 | along with this program. If not, see .
649 |
650 | Also add information on how to contact you by electronic and paper mail.
651 |
652 | If the program does terminal interaction, make it output a short
653 | notice like this when it starts in an interactive mode:
654 |
655 | {project} Copyright (C) {year} {fullname}
656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
657 | This is free software, and you are welcome to redistribute it
658 | under certain conditions; type `show c' for details.
659 |
660 | The hypothetical commands `show w' and `show c' should show the appropriate
661 | parts of the General Public License. Of course, your program's commands
662 | might be different; for a GUI interface, you would use an "about box".
663 |
664 | You should also get your employer (if you work as a programmer) or school,
665 | if any, to sign a "copyright disclaimer" for the program, if necessary.
666 | For more information on this, and how to apply and follow the GNU GPL, see
667 | .
668 |
669 | The GNU General Public License does not permit incorporating your program
670 | into proprietary programs. If your program is a subroutine library, you
671 | may consider it more useful to permit linking proprietary applications with
672 | the library. If this is what you want to do, use the GNU Lesser General
673 | Public License instead of this License. But first, please read
674 | .
--------------------------------------------------------------------------------
/MANIFEST.in:
--------------------------------------------------------------------------------
1 | graft src
2 | global-exclude .DS_Store
--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
1 | CC=gcc
2 | CFLAGS=
3 | LDFLAGS=
4 | SOURCES=src/main.c src/cdindex.c src/graph.c src/utility.c
5 | OBJECTS=$(SOURCES:.c=.o)
6 | EXECUTABLE=bin/cdindex
7 |
8 | all: $(SOURCES) $(EXECUTABLE)
9 |
10 | $(EXECUTABLE): $(OBJECTS)
11 | $(CC) $(LDFLAGS) $(OBJECTS) -o $@
12 |
13 | c.o:
14 | $(CC) $(CFLAGS) $< -o $@
15 |
16 | clean:
17 | rm src/*o
18 |
--------------------------------------------------------------------------------
/README.rst:
--------------------------------------------------------------------------------
1 | cdindex
2 | =======
3 |
4 | .. image:: https://readthedocs.org/projects/cdindex/badge/?version=latest
5 | :target: https://readthedocs.org/projects/cdindex/?badge=latest
6 | :alt: Documentation Status
7 |
8 | cdindex is a Python package, written in C, for computing the CD index and other dynamic
9 | measures on evolving directed graphs.
10 |
11 | - **Website:** http://www.cdindex.info
12 | - **Source:** https://github.com/russellfunk/cdindex
13 | - **Bug reports:**
14 |
15 | Install
16 | -------
17 |
18 | Install the latest version of cdindex::
19 |
20 | $ pip install cdindex
21 |
22 | Simple example
23 | --------------
24 |
25 | Create a graph with some dummy data and compute the CD index::
26 |
27 | >>> import cdindex
28 | >>> import datetime
29 | >>> from dateutil.relativedelta import relativedelta
30 |
31 | >>> def get_t_delta(vertex, years):
32 | vertex_datetime = cdindex.datetime_from_timestamp(graph.timestamp(vertex))
33 | future_datetime = vertex_datetime + relativedelta(years=years)
34 | difference = future_datetime - vertex_datetime
35 | return int(difference.total_seconds())
36 |
37 | >>> # dummy vertices for python module tests
38 | >>> pyvertices= [{"name": "0Z", "time": datetime.datetime(1992, 1, 1)},
39 | {"name": "1Z", "time": datetime.datetime(1992, 1, 1)},
40 | {"name": "2Z", "time": datetime.datetime(1993, 1, 1)},
41 | {"name": "3Z", "time": datetime.datetime(1993, 1, 1)},
42 | {"name": "4Z", "time": datetime.datetime(1995, 1, 1)},
43 | {"name": "5Z", "time": datetime.datetime(1997, 1, 1)},
44 | {"name": "6Z", "time": datetime.datetime(1998, 1, 1)},
45 | {"name": "7Z", "time": datetime.datetime(1999, 1, 1)},
46 | {"name": "8Z", "time": datetime.datetime(1999, 1, 1)},
47 | {"name": "9Z", "time": datetime.datetime(1998, 1, 1)},
48 | {"name": "10Z", "time": datetime.datetime(1997, 1, 1)}]
49 |
50 | >>> # dummy edges for python module tests
51 | >>> pyedges = [{"source": "4Z", "target": "2Z"},
52 | {"source": "4Z", "target": "0Z"},
53 | {"source": "4Z", "target": "1Z"},
54 | {"source": "4Z", "target": "3Z"},
55 | {"source": "5Z", "target": "2Z"},
56 | {"source": "6Z", "target": "2Z"},
57 | {"source": "6Z", "target": "4Z"},
58 | {"source": "7Z", "target": "4Z"},
59 | {"source": "8Z", "target": "4Z"},
60 | {"source": "9Z", "target": "4Z"},
61 | {"source": "9Z", "target": "1Z"},
62 | {"source": "9Z", "target": "3Z"},
63 | {"source": "10Z", "target": "4Z"}]
64 |
65 |
66 | >>> # create graph
67 | >>> graph = cdindex.Graph()
68 |
69 | >>> # add vertices
70 | >>> for vertex in pyvertices:
71 | graph.add_vertex(vertex["name"], cdindex.timestamp_from_datetime(vertex["time"]))
72 |
73 | >>> # add edges
74 | >>> for edge in pyedges:
75 | graph.add_edge(edge["source"], edge["target"])
76 |
77 | >>> graph.cdindex("4Z", get_t_delta("4Z", years=5))
78 |
79 | >>> graph.mcdindex("4Z", get_t_delta("4Z", years=5))
80 |
81 | Bugs
82 | ----
83 |
84 | Please report any bugs to .
85 |
86 | License
87 | -------
88 |
89 | Released under the GNU General Public License (GPL) (see `LICENSE`)::
90 |
91 | Copyright (C) 2024 Russell J. Funk
92 |
93 | Other implementations
94 | ---------------------
95 |
96 | Below is a list of other (known) implementations of the cdindex. Please contact us if you know of others.
97 |
98 | * novelpy (https://novelpy.readthedocs.io/en/latest/index.html)
99 | * fast-cdindex (https://github.com/dspinellis/fast-cdindex)
100 |
--------------------------------------------------------------------------------
/cdindex/__init__.py:
--------------------------------------------------------------------------------
1 | try:
2 | from cdindex.cdindex import *
3 | except ImportError:
4 | from cdindex import *
5 |
6 | try:
7 | from cdindex.time_utilities import *
8 | except ImportError:
9 | from time_utilities import *
--------------------------------------------------------------------------------
/cdindex/cdindex.py:
--------------------------------------------------------------------------------
1 | #!/usr/local/bin/python
2 | # -*- coding: utf-8 -*-
3 |
4 | """cdindex.py: This script is an interface for the c extension _cdindex."""
5 |
6 | __author__ = "Russell J. Funk"
7 | __copyright__ = "Copyright (C) 2019"
8 |
9 | # built in modules
10 | import math
11 | import random
12 | import itertools
13 | import os
14 |
15 | try:
16 | from builtins import int
17 | except ImportError:
18 | from __builtin__ import int
19 |
20 | # custom modules
21 | if "READTHEDOCS" not in os.environ:
22 | try:
23 | import cdindex._cdindex as _cdindex
24 | except ImportError:
25 | import _cdindex
26 |
27 | try:
28 | import cdindex.time_utilities
29 | except ImportError:
30 | import time_utilities
31 |
32 | class Graph:
33 | """Create a graph.
34 |
35 | This class defines a graph data structure on which to compute the cdindex and other
36 | functions that are made available through the module.
37 | """
38 |
39 | def __init__(self, vertices=[], edges=[]):
40 | """Initialize a new graph.
41 |
42 | Create a new graph for analysis. Vertices and edges can be added either when the graph
43 | is initialized, or later.
44 |
45 | Example
46 | -------
47 | vs = [{"name": "0Z", "time": datetime.datetime(1992, 1, 1)},
48 | {"name": "1Z", "time": datetime.datetime(1992, 1, 1)},
49 | {"name": "2Z", "time": datetime.datetime(1993, 1, 1)},
50 | {"name": "3Z", "time": datetime.datetime(1993, 1, 1)},
51 | {"name": "4Z", "time": datetime.datetime(1995, 1, 1)},
52 | {"name": "5Z", "time": datetime.datetime(1997, 1, 1)},
53 | {"name": "6Z", "time": datetime.datetime(1998, 1, 1)},
54 | {"name": "7Z", "time": datetime.datetime(1999, 1, 1)},
55 | {"name": "8Z", "time": datetime.datetime(1999, 1, 1)},
56 | {"name": "9Z", "time": datetime.datetime(1998, 1, 1)},
57 | {"name": "10Z", "time": datetime.datetime(1997, 1, 1)}]
58 |
59 | es = [{"source": "4Z", "target": "2Z"},
60 | {"source": "4Z", "target": "0Z"},
61 | {"source": "4Z", "target": "1Z"},
62 | {"source": "4Z", "target": "3Z"},
63 | {"source": "5Z", "target": "2Z"},
64 | {"source": "6Z", "target": "2Z"},
65 | {"source": "6Z", "target": "4Z"},
66 | {"source": "7Z", "target": "4Z"},
67 | {"source": "8Z", "target": "4Z"},
68 | {"source": "9Z", "target": "4Z"},
69 | {"source": "9Z", "target": "1Z"},
70 | {"source": "9Z", "target": "3Z"},
71 | {"source": "10Z", "target": "4Z"}]
72 |
73 | graph = cdindex.Graph(vertices=vs, edges=es)
74 |
75 |
76 | Parameters
77 | ----------
78 | vertices :
79 | List of vertices with names and timestamps, e.g.,
80 | [{"name": "0Z", "time": datetime.datetime(1992, 1, 1)}].
81 | edges :
82 | List of edges with sources and targets, e.g., [{"source": "4Z", "target": "2Z"}].
83 | """
84 |
85 | self._graph = _cdindex.Graph()
86 | self._vertex_name_crosswalk = {}
87 | self._vertex_id_crosswalk = {}
88 |
89 | # add vertices
90 | for vertex in vertices:
91 | self.add_vertex(vertex["name"], vertex["time"])
92 |
93 | # add edges
94 | for edge in edges:
95 | self.add_edge(edge["source"], edge["target"])
96 |
97 | def add_vertex(self, name, t):
98 | """Add a new vertex to the graph.
99 |
100 | This function adds a new vertex to the graph, given a name and timestamp.
101 |
102 | Parameters
103 | ----------
104 | name :
105 | The vertex name.
106 | t : int
107 | The vertex timestamp.
108 | """
109 | vertex_id = self.vcount()
110 | if name in self._vertex_name_crosswalk:
111 | raise ValueError("Vertex already added to graph")
112 | else:
113 | self._vertex_name_crosswalk[name] = vertex_id
114 | self._vertex_id_crosswalk[vertex_id] = name
115 | if isinstance(t, (int)) is False:
116 | raise ValueError("Time (t) of vertex must be an integer or long")
117 |
118 | # add the vertex
119 | _cdindex.add_vertex(self._graph, vertex_id, t)
120 |
121 | def add_edge(self, source_name, target_name):
122 | """Add a new edge to the graph.
123 |
124 | This function adds a new edge to the graph, given a source name and target
125 | name.
126 |
127 | Parameters
128 | ----------
129 | source_name :
130 | The source vertex name.
131 | target_name :
132 | The target vertex timestamp.
133 | """
134 | if (source_name not in self._vertex_name_crosswalk
135 | or target_name not in self._vertex_name_crosswalk):
136 | raise ValueError("One or more vertices are not in the graph")
137 | elif (target_name in self.out_edges(source_name)):
138 | raise ValueError("The edge being added is already in the graph")
139 | else:
140 | _cdindex.add_edge(self._graph,
141 | self._vertex_name_crosswalk[source_name],
142 | self._vertex_name_crosswalk[target_name])
143 |
144 | def vcount(self):
145 | """Return the number of vertices in the graph.
146 |
147 | This function returns the number of vertices in the graph. Note that time is
148 | not taken into account. The total count of vertices are returned regardless
149 | of when they appear in the graph.
150 |
151 | Returns
152 | -------
153 | int
154 | The number of vertices.
155 | """
156 | return _cdindex.get_vcount(self._graph)
157 |
158 | def _c_vertices(self):
159 | """Return the ids of the vertices in the graph from the C extension.
160 |
161 | This function returns a list of vertices in the graph. Rather than returning
162 | names, the id numbers from the C extension are returned. This function is
163 | not useful other than for internal purpuses. Note that time is not taken
164 | into account. Vertices are returned regardless of when they appear in the
165 | graph.
166 |
167 | Returns
168 | -------
169 | list
170 | The vertices.
171 | """
172 | return _cdindex.get_vertices(self._graph)
173 |
174 | def vertices(self):
175 | """Return the vertices in the graph.
176 |
177 | This function returns a list of vertices in the graph. Note that time is not
178 | taken into account. Vertices are returned regardless of when they appear in
179 | the graph.
180 |
181 | Returns
182 | -------
183 | list
184 | The vertices.
185 | """
186 | return self._vertex_name_crosswalk.keys()
187 |
188 | def ecount(self):
189 | """Return the number of edges in the graph.
190 |
191 | This function returns the number of edges in the graph. Note that time is
192 | not taken into account. The total count of edges are returned regardless of
193 | when they appear in the graph.
194 |
195 | Returns
196 | -------
197 | int
198 | The number of edges.
199 | """
200 | return _cdindex.get_ecount(self._graph)
201 |
202 | def in_degree(self, name):
203 | """Return the in degree of the focal vertex.
204 |
205 | Given a vertex, this function returns its in degree centrality, i.e., the
206 | number of other vertices in the graph that cite the focal vertex. Note that
207 | time is not taken into account. The function counts edges regardless of when
208 | they appear in the graph.
209 |
210 | Parameters
211 | ----------
212 | name :
213 | The vertex name.
214 |
215 | Returns
216 | -------
217 | int
218 | The in degree centrality.
219 | """
220 | return _cdindex.get_vertex_in_degree(self._graph,
221 | self._vertex_name_crosswalk[name])
222 |
223 | def in_edges(self, name):
224 | """Return the in edges of the focal vertex.
225 |
226 | Given a vertex, this function returns its in edges, i.e., the other
227 | vertices in the graph cited by the focal vertex. Note that time is not taken
228 | into account. The function returns edges regardless of when they appear in
229 | the graph.
230 |
231 | Parameters
232 | ----------
233 | name :
234 | The vertex name.
235 |
236 | Returns
237 | -------
238 | list
239 | The in edges.
240 | """
241 | in_edges_ids = _cdindex.get_vertex_in_edges(self._graph,
242 | self._vertex_name_crosswalk[name])
243 | return [self._vertex_id_crosswalk[vertex_id] for vertex_id in in_edges_ids]
244 |
245 | def out_degree(self, name):
246 | """Return the out degree of the focal vertex.
247 |
248 | Given a vertex, this function returns its out degree centrality, i.e., the
249 | number of other vertices in the graph cited by the focal vertex. Note that
250 | time is not taken into account. The function counts edges regardless of when
251 | they appear in the graph.
252 |
253 | Parameters
254 | ----------
255 | name :
256 | The vertex name.
257 |
258 | Returns
259 | -------
260 | int
261 | The out degree centrality.
262 | """
263 | return _cdindex.get_vertex_out_degree(self._graph,
264 | self._vertex_name_crosswalk[name])
265 |
266 | def out_edges(self, name):
267 | """Return the out edges of the focal vertex.
268 |
269 | Given a vertex, this function returns its out edges, i.e., the other
270 | vertices in the graph cited by the focal vertex. Note that time is not taken
271 | into account. The function returns edges regardless of when they appear in
272 | the graph.
273 |
274 | Parameters
275 | ----------
276 | name :
277 | The vertex name.
278 |
279 | Returns
280 | -------
281 | list
282 | The out edges.
283 | """
284 | out_edges_ids = _cdindex.get_vertex_out_edges(self._graph,
285 | self._vertex_name_crosswalk[name])
286 | return [self._vertex_id_crosswalk[vertex_id] for vertex_id in out_edges_ids]
287 |
288 | def timestamp(self, name):
289 | """Return the timestamp of the focal vertex.
290 |
291 | Given a vertex, this function returns its timestamp.
292 |
293 | Parameters
294 | ----------
295 | name :
296 | The vertex name.
297 |
298 | Returns
299 | -------
300 | int
301 | The timestamp.
302 | """
303 | return _cdindex.get_vertex_timestamp(self._graph,
304 | self._vertex_name_crosswalk[name])
305 |
306 | def cdindex(self, name, t_delta):
307 | """Compute the CD index.
308 |
309 | This function computes the CD index for a specified vertex at a given
310 | t_delta, where t_delta is an integer that gives the positive distance in
311 | time from the timestamp of the focal node when the index should be
312 | calculated.
313 |
314 | Parameters
315 | ----------
316 | t_delta : int
317 | A time delta.
318 |
319 | Returns
320 | -------
321 | double
322 | The CD index.
323 | """
324 | if isinstance(t_delta, (int)) is False:
325 | raise ValueError("Time delta (t_delta) must be an integer or long")
326 | result = _cdindex.cdindex(self._graph,
327 | self._vertex_name_crosswalk[name],
328 | t_delta)
329 | if math.isnan(result):
330 | return None
331 | else:
332 | return result
333 |
334 | def mcdindex(self, name, t_delta):
335 | """Compute the mCD index.
336 |
337 | This function computes the mCD index for a specified vertex at a given
338 | t_delta, where t_delta is an integer that gives the positive distance in
339 | time from the timestamp of the focal node when the index should be
340 | calculated.
341 |
342 | Parameters
343 | ----------
344 | t_delta : int
345 | A time delta.
346 |
347 | Returns
348 | -------
349 | double
350 | The mCD index.
351 | """
352 | if isinstance(t_delta, (int)) is False:
353 | raise ValueError("Time delta (t_delta) must be an integer or long")
354 |
355 | result = _cdindex.mcdindex(self._graph,
356 | self._vertex_name_crosswalk[name],
357 | t_delta)
358 | if math.isnan(result):
359 | return None
360 | else:
361 | return result
362 |
363 | def iindex(self, name, t_delta):
364 | """Compute the I index.
365 |
366 | This function computes the I index for a specified vertex at a given
367 | t_delta, where t_delta is an integer that gives the positive distance in
368 | time from the timestamp of the focal node when the index should be
369 | calculated. The I index is the in degree of the focal node at time t.
370 |
371 | Parameters
372 | ----------
373 | t_delta : int
374 | A time delta.
375 |
376 | Returns
377 | -------
378 | double
379 | The I index.
380 | """
381 | if isinstance(t_delta, (int)) is False:
382 | raise ValueError("Time delta (t_delta) must be an integer or long")
383 | return _cdindex.iindex(self._graph,
384 | self._vertex_name_crosswalk[name],
385 | t_delta)
386 |
387 | def _is_graph_sane(self):
388 | """Test graph sanity.
389 |
390 | Run tests to verify the internal graph storage structure. Not really a
391 | useful function other than for checking possible issues with the module.
392 |
393 | Returns
394 | -------
395 | bool
396 | True if successful, False otherwise.
397 | """
398 | return _cdindex._is_graph_sane(self._graph)
399 |
400 | class RandomGraph(Graph):
401 | """Create a random graph.
402 |
403 | This class generates a random graph that can be used for testing the cdindex and other
404 | functions that are made available through the module.
405 | """
406 |
407 | def __init__(self, generations=[], edge_fraction=[]):
408 | """Initialize a new random graph.
409 |
410 | Create a new random graph for analysis.
411 |
412 | Example
413 | -------
414 | graph = cdindex.RandomGraph(generations=(2,3,4,5,6,7,7,9), edge_fraction=1)
415 |
416 | Parameters
417 | ----------
418 | generations :
419 | List of discrete "generations", i.e., timestamps for each vertex.
420 | edge_fraction :
421 | The fraction of edges that should be present in the graph.
422 | """
423 |
424 | # build vertex list
425 | vertices = []
426 | for generation_id, generation_size in enumerate(generations):
427 | new_vertices = range(generation_size)
428 | vertices.extend([{"name": "v" + str(nv) + "g" + str(generation_id),
429 | "time": generation_id} for nv in new_vertices])
430 |
431 | # build edge list
432 | edges = []
433 | for possible_edges in itertools.product(vertices, vertices):
434 | if possible_edges[0]["time"] > possible_edges[1]["time"]:
435 | edges.append({"source": possible_edges[0]["name"],
436 | "target": possible_edges[1]["name"]})
437 |
438 | # pull fraction of edges to keep
439 | random.shuffle(edges)
440 | edges = edges[0:int(math.ceil(edge_fraction * len(edges)))]
441 |
442 | # initialize graph
443 | Graph.__init__(self, vertices, edges)
444 |
445 | def main():
446 |
447 | return None
448 |
449 | if __name__ == '__main__':
450 | main()
451 |
--------------------------------------------------------------------------------
/cdindex/pycdindex.c:
--------------------------------------------------------------------------------
1 | /*
2 | cdindex library.
3 | Copyright (C) 2017 Russell J. Funk
4 |
5 | This program is free software: you can redistribute it and/or modify
6 | it under the terms of the GNU General Public License as published by
7 | the Free Software Foundation, either version 3 of the License, or
8 | (at your option) any later version.
9 |
10 | This program is distributed in the hope that it will be useful,
11 | but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | GNU General Public License for more details.
14 |
15 | You should have received a copy of the GNU General Public License
16 | along with this program. If not, see .
17 | */
18 |
19 | #include
20 | #include "cdindex.h"
21 |
22 | #if PY_MAJOR_VERSION >= 3
23 | #define PY3K
24 | #endif
25 |
26 | /* Destructor function for Graph */
27 | static void del_Graph(PyObject *obj) {
28 | free_graph(PyCapsule_GetPointer(obj,"Graph"));
29 | free(PyCapsule_GetPointer(obj,"Graph"));
30 | }
31 |
32 | /* Graph utility functions */
33 | static Graph *PyGraph_AsGraph(PyObject *obj) {
34 | return (Graph *) PyCapsule_GetPointer(obj, "Graph");
35 | }
36 | static PyObject *PyGraph_FromGraph(Graph *g, int must_free) {
37 | return PyCapsule_New(g, "Graph", must_free ? del_Graph : NULL);
38 | }
39 |
40 | /*******************************************************************************
41 | * Create a new Graph object *
42 | ******************************************************************************/
43 | static PyObject *py_Graph(PyObject *self, PyObject *args) {
44 | Graph *g;
45 |
46 | // create a graph
47 | g = (Graph *) malloc(sizeof(Graph));
48 | g->vcount = 0;
49 | g->ecount = 0;
50 |
51 | return PyGraph_FromGraph(g, 1);
52 | }
53 |
54 | /*******************************************************************************
55 | * Check graph sanity *
56 | ******************************************************************************/
57 | static PyObject *py_is_graph_sane(PyObject *self, PyObject *args) {
58 | Graph *g;
59 | PyObject *py_g;
60 |
61 | if (!PyArg_ParseTuple(args,"O",&py_g))
62 | return NULL;
63 | if (!(g = PyGraph_AsGraph(py_g)))
64 | return NULL;
65 |
66 | return Py_BuildValue("O", is_graph_sane(g) ? Py_True : Py_False);
67 | }
68 |
69 | /*******************************************************************************
70 | * Add a vertex to the graph *
71 | ******************************************************************************/
72 | static PyObject *py_add_vertex(PyObject *self, PyObject *args) {
73 | long long int ID;
74 | long long int TIMESTAMP;
75 | Graph *g;
76 | PyObject *py_g;
77 |
78 | if (!PyArg_ParseTuple(args,"OLL",&py_g, &ID, &TIMESTAMP))
79 | return NULL;
80 | if (!(g = PyGraph_AsGraph(py_g)))
81 | return NULL;
82 |
83 | add_vertex(g, ID, TIMESTAMP);
84 |
85 | return Py_BuildValue("");
86 | }
87 |
88 | /*******************************************************************************
89 | * Add an edge to the graph *
90 | ******************************************************************************/
91 | static PyObject *py_add_edge(PyObject *self, PyObject *args) {
92 | long long int SOURCE_ID, TARGET_ID;
93 | Graph *g;
94 | PyObject *py_g;
95 |
96 | if (!PyArg_ParseTuple(args,"OLL",&py_g, &SOURCE_ID, &TARGET_ID))
97 | return NULL;
98 | if (!(g = PyGraph_AsGraph(py_g)))
99 | return NULL;
100 |
101 | add_edge(g, SOURCE_ID, TARGET_ID);
102 |
103 | return Py_BuildValue("");
104 | }
105 |
106 | /*******************************************************************************
107 | * Get a count of vertices in the graph *
108 | ******************************************************************************/
109 | static PyObject *py_get_vcount(PyObject *self, PyObject *args) {
110 |
111 | Graph *g;
112 | PyObject *py_g;
113 |
114 | if (!PyArg_ParseTuple(args,"O",&py_g))
115 | return NULL;
116 | if (!(g = PyGraph_AsGraph(py_g)))
117 | return NULL;
118 |
119 | return Py_BuildValue("L", g->vcount);
120 | }
121 |
122 | /*******************************************************************************
123 | * Get list of vertices in the graph *
124 | ******************************************************************************/
125 | static PyObject *py_get_vertices(PyObject *self, PyObject *args) {
126 |
127 | Graph *g;
128 | PyObject *py_g, *id, *result;
129 |
130 | if (!PyArg_ParseTuple(args,"O",&py_g))
131 | return NULL;
132 | if (!(g = PyGraph_AsGraph(py_g)))
133 | return NULL;
134 |
135 | PyObject *vs_list = PyList_New(g->vcount);
136 |
137 | for (long long int i = 0; i < g->vcount; i++) {
138 | id = Py_BuildValue("L", g->vs[i].id);
139 | PyList_SetItem(vs_list, i, id);
140 | }
141 |
142 | result = Py_BuildValue("O", vs_list);
143 |
144 | // clean up
145 | Py_DECREF(vs_list);
146 |
147 | return result;
148 | }
149 |
150 | /*******************************************************************************
151 | * Get a count of edges in the graph *
152 | ******************************************************************************/
153 | static PyObject *py_get_ecount(PyObject *self, PyObject *args) {
154 |
155 | Graph *g;
156 | PyObject *py_g;
157 |
158 | if (!PyArg_ParseTuple(args,"O",&py_g))
159 | return NULL;
160 | if (!(g = PyGraph_AsGraph(py_g)))
161 | return NULL;
162 |
163 | return Py_BuildValue("L", g->ecount);
164 | }
165 |
166 | /*******************************************************************************
167 | * Get a vertex timestamp *
168 | ******************************************************************************/
169 | static PyObject *py_get_vertex_timestamp(PyObject *self, PyObject *args) {
170 | long long int ID;
171 |
172 | Graph *g;
173 | PyObject *py_g;
174 |
175 | if (!PyArg_ParseTuple(args,"OL",&py_g, &ID))
176 | return NULL;
177 | if (!(g = PyGraph_AsGraph(py_g)))
178 | return NULL;
179 |
180 | return Py_BuildValue("L", g->vs[ID].timestamp);
181 | }
182 |
183 | /*******************************************************************************
184 | * Get a vertex in degree *
185 | ******************************************************************************/
186 | static PyObject *py_get_vertex_in_degree(PyObject *self, PyObject *args) {
187 | long long int ID;
188 |
189 | Graph *g;
190 | PyObject *py_g;
191 |
192 | if (!PyArg_ParseTuple(args,"OL",&py_g, &ID))
193 | return NULL;
194 | if (!(g = PyGraph_AsGraph(py_g)))
195 | return NULL;
196 |
197 | return Py_BuildValue("L", g->vs[ID].in_degree);
198 | }
199 |
200 | /*******************************************************************************
201 | * Get the in edges of a vertex *
202 | ******************************************************************************/
203 | static PyObject *py_get_vertex_in_edges(PyObject *self, PyObject *args) {
204 |
205 | long long int ID;
206 | Graph *g;
207 | PyObject *py_g, *source_id, *result;
208 |
209 | if (!PyArg_ParseTuple(args,"OL",&py_g, &ID))
210 | return NULL;
211 | if (!(g = PyGraph_AsGraph(py_g)))
212 | return NULL;
213 |
214 | PyObject *vs_list = PyList_New(g->vs[ID].in_degree);
215 |
216 | for (long long int i = 0; i < g->vs[ID].in_degree; i++) {
217 | source_id = Py_BuildValue("L", g->vs[ID].in_edges[i]);
218 | PyList_SetItem(vs_list, i, source_id);
219 | }
220 |
221 | result = Py_BuildValue("O", vs_list);
222 |
223 | // clean up
224 | Py_DECREF(vs_list);
225 |
226 | return result;
227 | }
228 |
229 | /*******************************************************************************
230 | * Get a vertex out degree *
231 | ******************************************************************************/
232 | static PyObject *py_get_vertex_out_degree(PyObject *self, PyObject *args) {
233 | long long int ID;
234 |
235 | Graph *g;
236 | PyObject *py_g;
237 |
238 | if (!PyArg_ParseTuple(args,"OL",&py_g, &ID))
239 | return NULL;
240 | if (!(g = PyGraph_AsGraph(py_g)))
241 | return NULL;
242 |
243 | return Py_BuildValue("L", g->vs[ID].out_degree);
244 | }
245 |
246 | /*******************************************************************************
247 | * Get the out edges of a vertex *
248 | ******************************************************************************/
249 | static PyObject *py_get_vertex_out_edges(PyObject *self, PyObject *args) {
250 |
251 | long long int ID;
252 | Graph *g;
253 | PyObject *py_g, *target_id, *result;
254 |
255 | if (!PyArg_ParseTuple(args,"OL",&py_g, &ID))
256 | return NULL;
257 | if (!(g = PyGraph_AsGraph(py_g)))
258 | return NULL;
259 |
260 | PyObject *vs_list = PyList_New(g->vs[ID].out_degree);
261 |
262 | for (long long int i = 0; i < g->vs[ID].out_degree; i++) {
263 | target_id = Py_BuildValue("L", g->vs[ID].out_edges[i]);
264 | PyList_SetItem(vs_list, i, target_id);
265 | }
266 |
267 | result = Py_BuildValue("O", vs_list);
268 |
269 | // clean up
270 | Py_DECREF(vs_list);
271 |
272 | return result;
273 | }
274 |
275 | /*******************************************************************************
276 | * Compute the CD index *
277 | ******************************************************************************/
278 | static PyObject *py_cdindex(PyObject *self, PyObject *args) {
279 | long long int ID;
280 | long long int TIMESTAMP;
281 |
282 | double result;
283 | Graph *g;
284 | PyObject *py_g;
285 |
286 | if (!PyArg_ParseTuple(args,"OLL",&py_g, &ID, &TIMESTAMP))
287 | return NULL;
288 | if (!(g = PyGraph_AsGraph(py_g)))
289 | return NULL;
290 |
291 | result = cdindex(g, ID, TIMESTAMP);
292 |
293 | return Py_BuildValue("d", result);
294 | }
295 |
296 | /*******************************************************************************
297 | * Compute the mCD index *
298 | ******************************************************************************/
299 | static PyObject *py_mcdindex(PyObject *self, PyObject *args) {
300 | long long int ID;
301 | long long int TIMESTAMP;
302 | double result;
303 | Graph *g;
304 | PyObject *py_g;
305 |
306 | if (!PyArg_ParseTuple(args,"OLL",&py_g, &ID, &TIMESTAMP))
307 | return NULL;
308 | if (!(g = PyGraph_AsGraph(py_g)))
309 | return NULL;
310 |
311 | result = mcdindex(g, ID, TIMESTAMP);
312 |
313 | return Py_BuildValue("d", result);
314 | }
315 |
316 | /*******************************************************************************
317 | * Compute the I index *
318 | ******************************************************************************/
319 | static PyObject *py_iindex(PyObject *self, PyObject *args) {
320 | long long int ID;
321 | long long int TIMESTAMP;
322 | double result;
323 | Graph *g;
324 | PyObject *py_g;
325 |
326 | if (!PyArg_ParseTuple(args,"OLL",&py_g, &ID, &TIMESTAMP))
327 | return NULL;
328 | if (!(g = PyGraph_AsGraph(py_g)))
329 | return NULL;
330 |
331 | result = iindex(g, ID, TIMESTAMP);
332 |
333 | return Py_BuildValue("d", result);
334 | }
335 |
336 |
337 | /*******************************************************************************
338 | * Module method table *
339 | ******************************************************************************/
340 | static PyMethodDef CDIndexMethods[] = {
341 | {"Graph", py_Graph, METH_VARARGS, "Make a graph"},
342 | {"_is_graph_sane", py_is_graph_sane, METH_VARARGS, "Test graph sanity"},
343 | {"add_vertex", py_add_vertex, METH_VARARGS, "Add a vertex to a graph"},
344 | {"add_edge", py_add_edge, METH_VARARGS, "Add an edge to a graph"},
345 | {"get_vertices", py_get_vertices, METH_VARARGS, "Get a list of vertices in the graph"},
346 | {"get_vcount", py_get_vcount, METH_VARARGS, "Get the number of vertices in the graph"},
347 | {"get_ecount", py_get_ecount, METH_VARARGS, "Get the number of edges in the graph"},
348 | {"get_vertex_timestamp", py_get_vertex_timestamp, METH_VARARGS, "Get the timestamp of a vertex"},
349 | {"get_vertex_in_degree", py_get_vertex_in_degree, METH_VARARGS, "Get the in degree of a vertex"},
350 | {"get_vertex_in_edges", py_get_vertex_in_edges, METH_VARARGS, "Get the in edges of a vertex"},
351 | {"get_vertex_out_degree", py_get_vertex_out_degree, METH_VARARGS, "Get the out degree of a vertex"},
352 | {"get_vertex_out_edges", py_get_vertex_out_edges, METH_VARARGS, "Get the out edges of a vertex"},
353 | {"cdindex", py_cdindex, METH_VARARGS, "Compute the CD index"},
354 | {"mcdindex", py_mcdindex, METH_VARARGS, "Compute the mCD index"},
355 | {"iindex", py_iindex, METH_VARARGS, "Compute the I index"},
356 | { NULL, NULL, 0, NULL}
357 | };
358 |
359 | /*******************************************************************************
360 | * Module initialization function *
361 | ******************************************************************************/
362 |
363 |
364 | #ifdef PY3K
365 | static struct PyModuleDef _cdindex =
366 | {
367 | PyModuleDef_HEAD_INIT,
368 | "_cdindex",
369 | "",
370 | -1,
371 | CDIndexMethods
372 | };
373 |
374 | PyMODINIT_FUNC PyInit__cdindex(void)
375 | {
376 | return PyModule_Create(&_cdindex);
377 | }
378 | #else
379 | PyMODINIT_FUNC
380 | init_cdindex(void) {
381 | (void) Py_InitModule("_cdindex", CDIndexMethods);
382 | }
383 | #endif
--------------------------------------------------------------------------------
/cdindex/time_utilities.py:
--------------------------------------------------------------------------------
1 | #!/usr/local/bin/python
2 | # -*- coding: utf-8 -*-
3 |
4 | """time_utilities.py: Utility functions for converting time formats."""
5 |
6 | __author__ = "Russell J. Funk"
7 | __copyright__ = "Copyright (C) 2017"
8 |
9 | # built in modules
10 | import datetime
11 | import calendar
12 |
13 | def timestamp_from_datetime(dt):
14 | """Convert a datetime to a Unix timestamp.
15 |
16 | Given a datetime, this function returns a Unix timestamp. Input is assumed to
17 | be Greenwich Mean Time (GMT) and local time zone information is ignored. The
18 | function is useful for converting dates to integers, which are required as
19 | input to some other functions in the module.
20 |
21 | Parameters
22 | ----------
23 | dt : datetime
24 | A datetime.
25 |
26 | Returns
27 | -------
28 | int
29 | A Unix timestamp.
30 | """
31 | return calendar.timegm(dt.utctimetuple())
32 |
33 | def datetime_from_timestamp(ts):
34 | """Convert a Unix timestamp to a datetime.
35 |
36 | Given a Unix timestamp, this function returns a datetime. Input is assumed to
37 | be Greenwich Mean Time (GMT) and local time zone information is ignored. The
38 | function is useful for converting integers, which are required by some
39 | functions in the module, to more human readable dates.
40 |
41 | Parameters
42 | ----------
43 | ts : int
44 | A Unix timestamp.
45 |
46 | Returns
47 | -------
48 | datetime
49 | A datetime.
50 | """
51 | return datetime.datetime.utcfromtimestamp(ts)
52 |
53 | def main():
54 |
55 | return None
56 |
57 | if __name__ == "__main__":
58 | main()
--------------------------------------------------------------------------------
/docs/Makefile:
--------------------------------------------------------------------------------
1 | # Makefile for Sphinx documentation
2 | #
3 |
4 | # You can set these variables from the command line.
5 | SPHINXOPTS =
6 | SPHINXBUILD = sphinx-build
7 | PAPER =
8 | BUILDDIR = _build
9 |
10 | # User-friendly check for sphinx-build
11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
13 | endif
14 |
15 | # Internal variables.
16 | PAPEROPT_a4 = -D latex_paper_size=a4
17 | PAPEROPT_letter = -D latex_paper_size=letter
18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
19 | # the i18n builder cannot share the environment and doctrees with the others
20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
21 |
22 | .PHONY: help
23 | help:
24 | @echo "Please use \`make ' where is one of"
25 | @echo " html to make standalone HTML files"
26 | @echo " dirhtml to make HTML files named index.html in directories"
27 | @echo " singlehtml to make a single large HTML file"
28 | @echo " pickle to make pickle files"
29 | @echo " json to make JSON files"
30 | @echo " htmlhelp to make HTML files and a HTML help project"
31 | @echo " qthelp to make HTML files and a qthelp project"
32 | @echo " applehelp to make an Apple Help Book"
33 | @echo " devhelp to make HTML files and a Devhelp project"
34 | @echo " epub to make an epub"
35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
36 | @echo " latexpdf to make LaTeX files and run them through pdflatex"
37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
38 | @echo " text to make text files"
39 | @echo " man to make manual pages"
40 | @echo " texinfo to make Texinfo files"
41 | @echo " info to make Texinfo files and run them through makeinfo"
42 | @echo " gettext to make PO message catalogs"
43 | @echo " changes to make an overview of all changed/added/deprecated items"
44 | @echo " xml to make Docutils-native XML files"
45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes"
46 | @echo " linkcheck to check all external links for integrity"
47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)"
48 | @echo " coverage to run coverage check of the documentation (if enabled)"
49 |
50 | .PHONY: clean
51 | clean:
52 | rm -rf $(BUILDDIR)/*
53 |
54 | .PHONY: html
55 | html:
56 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
57 | @echo
58 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
59 |
60 | .PHONY: dirhtml
61 | dirhtml:
62 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
63 | @echo
64 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
65 |
66 | .PHONY: singlehtml
67 | singlehtml:
68 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
69 | @echo
70 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
71 |
72 | .PHONY: pickle
73 | pickle:
74 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
75 | @echo
76 | @echo "Build finished; now you can process the pickle files."
77 |
78 | .PHONY: json
79 | json:
80 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
81 | @echo
82 | @echo "Build finished; now you can process the JSON files."
83 |
84 | .PHONY: htmlhelp
85 | htmlhelp:
86 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
87 | @echo
88 | @echo "Build finished; now you can run HTML Help Workshop with the" \
89 | ".hhp project file in $(BUILDDIR)/htmlhelp."
90 |
91 | .PHONY: qthelp
92 | qthelp:
93 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
94 | @echo
95 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \
96 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
97 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/cdindex.qhcp"
98 | @echo "To view the help file:"
99 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/cdindex.qhc"
100 |
101 | .PHONY: applehelp
102 | applehelp:
103 | $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
104 | @echo
105 | @echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
106 | @echo "N.B. You won't be able to view it unless you put it in" \
107 | "~/Library/Documentation/Help or install it in your application" \
108 | "bundle."
109 |
110 | .PHONY: devhelp
111 | devhelp:
112 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
113 | @echo
114 | @echo "Build finished."
115 | @echo "To view the help file:"
116 | @echo "# mkdir -p $$HOME/.local/share/devhelp/cdindex"
117 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/cdindex"
118 | @echo "# devhelp"
119 |
120 | .PHONY: epub
121 | epub:
122 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
123 | @echo
124 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
125 |
126 | .PHONY: latex
127 | latex:
128 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
129 | @echo
130 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
131 | @echo "Run \`make' in that directory to run these through (pdf)latex" \
132 | "(use \`make latexpdf' here to do that automatically)."
133 |
134 | .PHONY: latexpdf
135 | latexpdf:
136 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
137 | @echo "Running LaTeX files through pdflatex..."
138 | $(MAKE) -C $(BUILDDIR)/latex all-pdf
139 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
140 |
141 | .PHONY: latexpdfja
142 | latexpdfja:
143 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
144 | @echo "Running LaTeX files through platex and dvipdfmx..."
145 | $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
146 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
147 |
148 | .PHONY: text
149 | text:
150 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
151 | @echo
152 | @echo "Build finished. The text files are in $(BUILDDIR)/text."
153 |
154 | .PHONY: man
155 | man:
156 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
157 | @echo
158 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
159 |
160 | .PHONY: texinfo
161 | texinfo:
162 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
163 | @echo
164 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
165 | @echo "Run \`make' in that directory to run these through makeinfo" \
166 | "(use \`make info' here to do that automatically)."
167 |
168 | .PHONY: info
169 | info:
170 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
171 | @echo "Running Texinfo files through makeinfo..."
172 | make -C $(BUILDDIR)/texinfo info
173 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
174 |
175 | .PHONY: gettext
176 | gettext:
177 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
178 | @echo
179 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
180 |
181 | .PHONY: changes
182 | changes:
183 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
184 | @echo
185 | @echo "The overview file is in $(BUILDDIR)/changes."
186 |
187 | .PHONY: linkcheck
188 | linkcheck:
189 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
190 | @echo
191 | @echo "Link check complete; look for any errors in the above output " \
192 | "or in $(BUILDDIR)/linkcheck/output.txt."
193 |
194 | .PHONY: doctest
195 | doctest:
196 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
197 | @echo "Testing of doctests in the sources finished, look at the " \
198 | "results in $(BUILDDIR)/doctest/output.txt."
199 |
200 | .PHONY: coverage
201 | coverage:
202 | $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
203 | @echo "Testing of coverage in the sources finished, look at the " \
204 | "results in $(BUILDDIR)/coverage/python.txt."
205 |
206 | .PHONY: xml
207 | xml:
208 | $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
209 | @echo
210 | @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
211 |
212 | .PHONY: pseudoxml
213 | pseudoxml:
214 | $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
215 | @echo
216 | @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
217 |
--------------------------------------------------------------------------------
/docs/cdindex.cdindex.rst:
--------------------------------------------------------------------------------
1 | cdindex.cdindex module
2 | ======================
3 |
4 | .. automodule:: cdindex.cdindex
5 | :members:
6 | :undoc-members:
7 | :show-inheritance:
8 |
--------------------------------------------------------------------------------
/docs/cdindex.rst:
--------------------------------------------------------------------------------
1 | cdindex package
2 | ===============
3 |
4 | Submodules
5 | ----------
6 |
7 | .. toctree::
8 |
9 | cdindex.cdindex
10 | cdindex.time_utilities
11 |
12 | Module contents
13 | ---------------
14 |
15 | .. automodule:: cdindex
16 | :members:
17 | :undoc-members:
18 | :show-inheritance:
19 |
--------------------------------------------------------------------------------
/docs/cdindex.time_utilities.rst:
--------------------------------------------------------------------------------
1 | cdindex.time_utilities module
2 | =============================
3 |
4 | .. automodule:: cdindex.time_utilities
5 | :members:
6 | :undoc-members:
7 | :show-inheritance:
8 |
--------------------------------------------------------------------------------
/docs/conf.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | #
3 | # cdindex documentation build configuration file, created by
4 | # sphinx-quickstart on Tue Jul 11 13:27:32 2017.
5 | #
6 | # This file is execfile()d with the current directory set to its
7 | # containing dir.
8 | #
9 | # Note that not all possible configuration values are present in this
10 | # autogenerated file.
11 | #
12 | # All configuration values have a default; values that are commented out
13 | # serve to show the default.
14 |
15 | import sys
16 | import os
17 |
18 | import sys
19 | from mock import Mock as MagicMock
20 | class Mock(MagicMock):
21 | @classmethod
22 | def __getattr__(cls, name):
23 | return MagicMock()
24 | MOCK_MODULES = ['_cdindex']
25 | sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
26 |
27 |
28 | # If extensions (or modules to document with autodoc) are in another directory,
29 | # add these directories to sys.path here. If the directory is relative to the
30 | # documentation root, use os.path.abspath to make it absolute, like shown here.
31 | #sys.path.insert(0, os.path.abspath('.'))
32 | sys.path.insert(0, os.path.abspath("../"))
33 |
34 | # -- General configuration ------------------------------------------------
35 |
36 | # If your documentation needs a minimal Sphinx version, state it here.
37 | #needs_sphinx = '1.0'
38 |
39 | # Add any Sphinx extension module names here, as strings. They can be
40 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
41 | # ones.
42 | extensions = [
43 | 'sphinx.ext.autodoc',
44 | 'sphinx.ext.coverage',
45 | 'sphinx.ext.viewcode',
46 | 'sphinx.ext.napoleon'
47 | ]
48 |
49 | # Add any paths that contain templates here, relative to this directory.
50 | templates_path = ['_templates']
51 |
52 | # The suffix(es) of source filenames.
53 | # You can specify multiple suffix as a list of string:
54 | # source_suffix = ['.rst', '.md']
55 | source_suffix = '.rst'
56 |
57 | # The encoding of source files.
58 | #source_encoding = 'utf-8-sig'
59 |
60 | # The master toctree document.
61 | master_doc = 'index'
62 |
63 | # General information about the project.
64 | project = u'cdindex'
65 | copyright = u'2024, Russell J. Funk'
66 | author = u'Russell J. Funk'
67 |
68 | # The version info for the project you're documenting, acts as replacement for
69 | # |version| and |release|, also used in various other places throughout the
70 | # built documents.
71 | #
72 | # The short X.Y version.
73 | version = u'1.0'
74 | # The full version, including alpha/beta/rc tags.
75 | release = u'1.0.20'
76 |
77 | # The language for content autogenerated by Sphinx. Refer to documentation
78 | # for a list of supported languages.
79 | #
80 | # This is also used if you do content translation via gettext catalogs.
81 | # Usually you set "language" from the command line for these cases.
82 | language = None
83 |
84 | # There are two options for replacing |today|: either, you set today to some
85 | # non-false value, then it is used:
86 | #today = ''
87 | # Else, today_fmt is used as the format for a strftime call.
88 | #today_fmt = '%B %d, %Y'
89 |
90 | # List of patterns, relative to source directory, that match files and
91 | # directories to ignore when looking for source files.
92 | exclude_patterns = ['_build']
93 |
94 | # The reST default role (used for this markup: `text`) to use for all
95 | # documents.
96 | #default_role = None
97 |
98 | # If true, '()' will be appended to :func: etc. cross-reference text.
99 | #add_function_parentheses = True
100 |
101 | # If true, the current module name will be prepended to all description
102 | # unit titles (such as .. function::).
103 | #add_module_names = True
104 |
105 | # If true, sectionauthor and moduleauthor directives will be shown in the
106 | # output. They are ignored by default.
107 | #show_authors = False
108 |
109 | # The name of the Pygments (syntax highlighting) style to use.
110 | pygments_style = 'sphinx'
111 |
112 | # A list of ignored prefixes for module index sorting.
113 | #modindex_common_prefix = []
114 |
115 | # If true, keep warnings as "system message" paragraphs in the built documents.
116 | #keep_warnings = False
117 |
118 | # If true, `todo` and `todoList` produce output, else they produce nothing.
119 | todo_include_todos = False
120 |
121 |
122 | # -- Options for HTML output ----------------------------------------------
123 |
124 | # The theme to use for HTML and HTML Help pages. See the documentation for
125 | # a list of builtin themes.
126 | #html_theme = 'alabaster'
127 | html_theme = "sphinx_rtd_theme"
128 |
129 | # Theme options are theme-specific and customize the look and feel of a theme
130 | # further. For a list of options available for each theme, see the
131 | # documentation.
132 | #html_theme_options = {}
133 |
134 | # Add any paths that contain custom themes here, relative to this directory.
135 | #html_theme_path = []
136 |
137 | # The name for this set of Sphinx documents. If None, it defaults to
138 | # " v documentation".
139 | #html_title = None
140 |
141 | # A shorter title for the navigation bar. Default is the same as html_title.
142 | #html_short_title = None
143 |
144 | # The name of an image file (relative to this directory) to place at the top
145 | # of the sidebar.
146 | #html_logo = None
147 |
148 | # The name of an image file (within the static path) to use as favicon of the
149 | # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
150 | # pixels large.
151 | #html_favicon = None
152 |
153 | # Add any paths that contain custom static files (such as style sheets) here,
154 | # relative to this directory. They are copied after the builtin static files,
155 | # so a file named "default.css" will overwrite the builtin "default.css".
156 | html_static_path = ['_static']
157 |
158 | # Add any extra paths that contain custom files (such as robots.txt or
159 | # .htaccess) here, relative to this directory. These files are copied
160 | # directly to the root of the documentation.
161 | #html_extra_path = []
162 |
163 | # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
164 | # using the given strftime format.
165 | #html_last_updated_fmt = '%b %d, %Y'
166 |
167 | # If true, SmartyPants will be used to convert quotes and dashes to
168 | # typographically correct entities.
169 | #html_use_smartypants = True
170 |
171 | # Custom sidebar templates, maps document names to template names.
172 | #html_sidebars = {}
173 |
174 | # Additional templates that should be rendered to pages, maps page names to
175 | # template names.
176 | #html_additional_pages = {}
177 |
178 | # If false, no module index is generated.
179 | #html_domain_indices = True
180 |
181 | # If false, no index is generated.
182 | #html_use_index = True
183 |
184 | # If true, the index is split into individual pages for each letter.
185 | #html_split_index = False
186 |
187 | # If true, links to the reST sources are added to the pages.
188 | #html_show_sourcelink = True
189 |
190 | # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
191 | #html_show_sphinx = True
192 |
193 | # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
194 | #html_show_copyright = True
195 |
196 | # If true, an OpenSearch description file will be output, and all pages will
197 | # contain a tag referring to it. The value of this option must be the
198 | # base URL from which the finished HTML is served.
199 | #html_use_opensearch = ''
200 |
201 | # This is the file name suffix for HTML files (e.g. ".xhtml").
202 | #html_file_suffix = None
203 |
204 | # Language to be used for generating the HTML full-text search index.
205 | # Sphinx supports the following languages:
206 | # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
207 | # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
208 | #html_search_language = 'en'
209 |
210 | # A dictionary with options for the search language support, empty by default.
211 | # Now only 'ja' uses this config value
212 | #html_search_options = {'type': 'default'}
213 |
214 | # The name of a javascript file (relative to the configuration directory) that
215 | # implements a search results scorer. If empty, the default will be used.
216 | #html_search_scorer = 'scorer.js'
217 |
218 | # Output file base name for HTML help builder.
219 | htmlhelp_basename = 'cdindexdoc'
220 |
221 | # -- Options for LaTeX output ---------------------------------------------
222 |
223 | latex_elements = {
224 | # The paper size ('letterpaper' or 'a4paper').
225 | #'papersize': 'letterpaper',
226 |
227 | # The font size ('10pt', '11pt' or '12pt').
228 | #'pointsize': '10pt',
229 |
230 | # Additional stuff for the LaTeX preamble.
231 | #'preamble': '',
232 |
233 | # Latex figure (float) alignment
234 | #'figure_align': 'htbp',
235 | }
236 |
237 | # Grouping the document tree into LaTeX files. List of tuples
238 | # (source start file, target name, title,
239 | # author, documentclass [howto, manual, or own class]).
240 | latex_documents = [
241 | (master_doc, 'cdindex.tex', u'cdindex Documentation',
242 | u'Russell J. Funk', 'manual'),
243 | ]
244 |
245 | # The name of an image file (relative to this directory) to place at the top of
246 | # the title page.
247 | #latex_logo = None
248 |
249 | # For "manual" documents, if this is true, then toplevel headings are parts,
250 | # not chapters.
251 | #latex_use_parts = False
252 |
253 | # If true, show page references after internal links.
254 | #latex_show_pagerefs = False
255 |
256 | # If true, show URL addresses after external links.
257 | #latex_show_urls = False
258 |
259 | # Documents to append as an appendix to all manuals.
260 | #latex_appendices = []
261 |
262 | # If false, no module index is generated.
263 | #latex_domain_indices = True
264 |
265 |
266 | # -- Options for manual page output ---------------------------------------
267 |
268 | # One entry per manual page. List of tuples
269 | # (source start file, name, description, authors, manual section).
270 | man_pages = [
271 | (master_doc, 'cdindex', u'cdindex Documentation',
272 | [author], 1)
273 | ]
274 |
275 | # If true, show URL addresses after external links.
276 | #man_show_urls = False
277 |
278 |
279 | # -- Options for Texinfo output -------------------------------------------
280 |
281 | # Grouping the document tree into Texinfo files. List of tuples
282 | # (source start file, target name, title, author,
283 | # dir menu entry, description, category)
284 | texinfo_documents = [
285 | (master_doc, 'cdindex', u'cdindex Documentation',
286 | author, 'cdindex', 'One line description of project.',
287 | 'Miscellaneous'),
288 | ]
289 |
290 | # Documents to append as an appendix to all manuals.
291 | #texinfo_appendices = []
292 |
293 | # If false, no module index is generated.
294 | #texinfo_domain_indices = True
295 |
296 | # How to display URL addresses: 'footnote', 'no', or 'inline'.
297 | #texinfo_show_urls = 'footnote'
298 |
299 | # If true, do not generate a @detailmenu in the "Top" node's menu.
300 | #texinfo_no_detailmenu = False
301 |
--------------------------------------------------------------------------------
/docs/index.rst:
--------------------------------------------------------------------------------
1 | .. cdindex documentation master file, created by
2 | sphinx-quickstart on Tue Jul 11 15:29:31 2017.
3 | You can adapt this file completely to your liking, but it should at least
4 | contain the root `toctree` directive.
5 |
6 | Welcome to cdindex's documentation!
7 | ===================================
8 |
9 | Contents:
10 |
11 | .. toctree::
12 | :maxdepth: 2
13 |
14 |
15 |
16 | Indices and tables
17 | ==================
18 |
19 | * :ref:`genindex`
20 | * :ref:`modindex`
21 | * :ref:`search`
22 |
23 |
--------------------------------------------------------------------------------
/docs/modules.rst:
--------------------------------------------------------------------------------
1 | cdindex
2 | =======
3 |
4 | .. toctree::
5 | :maxdepth: 4
6 |
7 | cdindex
8 |
--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
1 | #!/usr/local/bin/python
2 | # -*- coding: utf-8 -*-
3 |
4 | """setup.py: This script installs the cdindex python module."""
5 |
6 | __author__ = "Russell J. Funk"
7 | __copyright__ = "Copyright (C) 2024"
8 |
9 | # built in modules
10 | from setuptools import setup, Extension, find_packages
11 |
12 | setup(name="cdindex",
13 | version="1.0.20",
14 | description="Package for computing the cdindex.",
15 | author="Russell J. Funk",
16 | author_email="russellfunk@gmail.com",
17 | url="http://www.cdindex.info",
18 | license="GNU General Public License (GPL)",
19 | install_requires=['future'],
20 | ext_modules=[
21 | Extension("cdindex._cdindex",
22 | ["src/cdindex.c",
23 | "src/graph.c",
24 | "src/utility.c",
25 | "cdindex/pycdindex.c"],
26 | include_dirs = ["src"],
27 | )
28 | ],
29 | packages=find_packages()
30 | )
31 |
32 | # python setup.py build_ext --inplace
33 | # python setup.py sdist
--------------------------------------------------------------------------------
/src/cdindex.c:
--------------------------------------------------------------------------------
1 | /*
2 | cdindex library.
3 | Copyright (C) 2017 Russell J. Funk
4 |
5 | This program is free software: you can redistribute it and/or modify
6 | it under the terms of the GNU General Public License as published by
7 | the Free Software Foundation, either version 3 of the License, or
8 | (at your option) any later version.
9 |
10 | This program is distributed in the hope that it will be useful,
11 | but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | GNU General Public License for more details.
14 |
15 | You should have received a copy of the GNU General Public License
16 | along with this program. If not, see .
17 | */
18 |
19 | #include
20 | #include
21 | #include "cdindex.h"
22 |
23 | /**
24 | * \function cdindex
25 | * \brief Computes the CD Index.
26 | *
27 | * \param graph The input graph.
28 | * \param id The focal vertex id.
29 | * \param time_delta Time beyond stamp of focal vertex to consider in measure.
30 | *
31 | * \return The value of the CD index.
32 | */
33 | double cdindex(Graph *graph, long long int id, long long int time_delta){
34 |
35 | /* Build a list of "it" vertices that are "in_edges" of the focal vertex's
36 | "out_edges" as of timestamp t. Vertices in the list are unique. */
37 |
38 | long long int it_count = 0;
39 | long long int *it = malloc(sizeof(long long int));
40 |
41 | /* check for malloc problems */
42 | if (it==NULL) {
43 | raise_error(0);
44 | }
45 |
46 | /* define i for multiple loops */
47 | long long int i;
48 |
49 | /* add unique "in_edges" of focal vertex "out_edges" */
50 | for (i = 0; i < graph->vs[id].out_degree; i++) {
51 | long long int out_edge_i = graph->vs[id].out_edges[i];
52 | for (long long int j = 0; j < graph->vs[out_edge_i].in_degree; j++) {
53 | long long int out_edge_i_in_edge_j = graph->vs[out_edge_i].in_edges[j];
54 | if (graph->vs[out_edge_i_in_edge_j].timestamp > graph->vs[id].timestamp &&
55 | graph->vs[out_edge_i_in_edge_j].timestamp <= (graph->vs[id].timestamp + time_delta) &&
56 | !in_int_array(it, it_count, out_edge_i_in_edge_j)) {
57 | add_to_int_array(&it, it_count, out_edge_i_in_edge_j, true);
58 | it_count++;
59 | }
60 | }
61 | }
62 |
63 | /* add unique "in_edges" of focal vertex */
64 | for (i = 0; i < graph->vs[id].in_degree; i++) {
65 | long long int in_edge_i = graph->vs[id].in_edges[i];
66 | if (graph->vs[in_edge_i].timestamp > graph->vs[id].timestamp &&
67 | graph->vs[in_edge_i].timestamp <= (graph->vs[id].timestamp + time_delta) &&
68 | !in_int_array(it, it_count, in_edge_i)) {
69 | add_to_int_array(&it, it_count, in_edge_i, true);
70 | it_count++;
71 | }
72 | }
73 |
74 | /* compute the cd index */
75 | double sum_i = 0.0;
76 | for (i = 0; i < it_count; i++) {
77 | long long int f_it = in_int_array(graph->vs[it[i]].out_edges, graph->vs[it[i]].out_degree, id);
78 | long long int b_it = 0;
79 | for (long long int j = 0; j < graph->vs[it[i]].out_degree; j++) {
80 | if (in_int_array(graph->vs[id].out_edges, graph->vs[id].out_degree, graph->vs[it[i]].out_edges[j])) {
81 | b_it = 1;
82 | }
83 | }
84 | sum_i += -2.0*f_it*b_it + f_it;
85 | }
86 |
87 | free(it);
88 | return sum_i/it_count;
89 | }
90 |
91 | /**
92 | * \function iindex
93 | * \brief Computes the I Index (i.e., the in degree of the focal vertex at time t).
94 | *
95 | * \param graph The input graph.
96 | * \param id The focal vertex id.
97 | * \param time_delta Time beyond stamp of focal vertex to consider in computing the measure.
98 | *
99 | * \return The value of the I index.
100 | */
101 | long long int iindex(Graph *graph, long long int id, long long int time_delta){
102 |
103 | /* count mt vertices that are "in_edges" of the focal vertex as of timestamp t. */
104 | long long int mt_count = 0;
105 | for (long long int i = 0; i < graph->vs[id].in_degree; i++) {
106 | long long int in_edge_i = graph->vs[id].in_edges[i];
107 | if (graph->vs[in_edge_i].timestamp <= (graph->vs[id].timestamp + time_delta)) {
108 | mt_count++;
109 | }
110 | }
111 |
112 | return mt_count;
113 | }
114 |
115 | /**
116 | * \function mcdindex
117 | * \brief Computes the mCD Index.
118 | *
119 | * \param graph The input graph.
120 | * \param id The focal vertex id.
121 | * \param time_delta Time beyond stamp of focal vertex to consider in computing the measure.
122 | *
123 | * \return The value of the mCD index.
124 | */
125 | double mcdindex(Graph *graph, long long int id, long long int time_delta){
126 |
127 | double cdindex_value = cdindex(graph, id, time_delta);
128 | long long int iindex_value = iindex(graph, id, time_delta);
129 |
130 | return cdindex_value * iindex_value;
131 |
132 | }
133 |
--------------------------------------------------------------------------------
/src/cdindex.h:
--------------------------------------------------------------------------------
1 | #include
2 |
3 | typedef struct Vertex {
4 | long long int id;
5 | long long int timestamp;
6 | long long int *in_edges;
7 | long long int *out_edges;
8 | long long int in_degree;
9 | long long int out_degree;
10 | } Vertex;
11 |
12 | typedef struct Edge {
13 | long long int source_id;
14 | long long int target_id;
15 | } Edge;
16 |
17 | typedef struct Graph {
18 | long long int vcount;
19 | Vertex *vs;
20 | long long int ecount;
21 | } Graph;
22 |
23 | #define CREATE_GRAPH(G) Graph G = {.vcount = 0, .ecount = 0}
24 |
25 | /* function prototypes for utility.c */
26 | void raise_error(int code);
27 | bool in_int_array(long long int *array, long long int sizeof_array, long long int value);
28 | void add_to_int_array(long long int **array, long long int sizeof_array, long long int value, bool add_memory);
29 |
30 | /* function prototypes for graph.c */
31 | bool is_graph_sane(Graph *graph);
32 | void add_vertex(Graph *graph, long long int id, long long int timestamp);
33 | void add_edge(Graph *graph, long long int source_id, long long int target_id);
34 | void free_graph(Graph *graph);
35 |
36 | /* function prototypes for cdindex.c */
37 | double cdindex(Graph *graph, long long int id, long long int time_delta);
38 | double mcdindex(Graph *graph, long long int id, long long int time_delta);
39 | long long int iindex(Graph *graph, long long int id, long long int time_delta);
40 |
--------------------------------------------------------------------------------
/src/graph.c:
--------------------------------------------------------------------------------
1 | /*
2 | cdindex library.
3 | Copyright (C) 2017 Russell J. Funk
4 |
5 | This program is free software: you can redistribute it and/or modify
6 | it under the terms of the GNU General Public License as published by
7 | the Free Software Foundation, either version 3 of the License, or
8 | (at your option) any later version.
9 |
10 | This program is distributed in the hope that it will be useful,
11 | but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | GNU General Public License for more details.
14 |
15 | You should have received a copy of the GNU General Public License
16 | along with this program. If not, see .
17 | */
18 |
19 | #include
20 | #include
21 | #include
22 | #include "cdindex.h"
23 |
24 | /**
25 | * \function is_graph_sane
26 | * \brief Run a few basic (not comprehensive) checks on graph data structure.
27 | *
28 | * \param graph The input graph.
29 | *
30 | * \return Whether the graph is sane.
31 | */
32 | bool is_graph_sane(Graph *graph) {
33 | bool sane = true;
34 |
35 | /* vcount should not be negative */
36 | if (graph->vcount < 0) {
37 | sane = false;
38 | }
39 | else {
40 | /* vertex ids should be sequential */
41 | if (graph->vcount > 1) {
42 | for (long long int i = 1; i < graph->vcount; i++) {
43 | if (graph->vs[i-1].id + 1 != graph->vs[i].id) {
44 | sane = false;
45 | }
46 | }
47 | }
48 | /* the last vertex id should correspond to the number of vertices - 1 */
49 | if (graph->vs[graph->vcount - 1].id != graph->vcount - 1) {
50 | sane = false;
51 | }
52 | }
53 | return sane;
54 | }
55 |
56 | /**
57 | * \function add_vertex
58 | * \brief Add a vertex to a graph (note the graph must have memory allocated).
59 | *
60 | * \param graph The input graph.
61 | * \param id The new vertex id.
62 | * \param timestamp The new vertex timestamp.
63 | */
64 | void add_vertex(Graph *graph, long long int id, long long int timestamp) {
65 |
66 | /* allocate memory for a vertex */
67 | Vertex *tmp;
68 | if (graph->vcount == 0) {
69 | tmp = malloc(sizeof(Vertex));
70 | }
71 | else {
72 | tmp = realloc(graph->vs, (graph->vcount + 1) * sizeof(Vertex));
73 | }
74 | if (tmp==NULL) {
75 | raise_error(0);
76 | }
77 | else {
78 | graph->vs = tmp;
79 | }
80 |
81 | /* the new vertex id should come at the end of the list */
82 | if (id != graph->vcount) {
83 | raise_error(1);
84 | }
85 | graph->vs[graph->vcount].id = graph->vcount;
86 | graph->vs[graph->vcount].timestamp = timestamp;
87 | graph->vs[graph->vcount].in_degree = 0;
88 | graph->vs[graph->vcount].out_degree = 0;
89 | graph->vcount++;
90 | }
91 |
92 | /**
93 | * \function add_edge
94 | * \brief Add a edge to a graph (note the graph must have memory allocated).
95 | *
96 | * \param graph The input graph.
97 | * \param source_id The source vertex id.
98 | * \param target_id The target vertex id.
99 | */
100 | void add_edge(Graph *graph, long long int source_id, long long int target_id) {
101 |
102 | /* confirm vertices are in graph */
103 | if (source_id >= graph->vcount || target_id >= graph->vcount) {
104 | raise_error(2);
105 | }
106 |
107 | /* confirm vertices are in graph */
108 | /*
109 | long long int vs_ids[graph->vcount];
110 | for (long long int i = 0; i < graph->vcount; i++) {
111 | vs_ids[i] = graph->vs[i].id;
112 | }
113 | if (!in_int_array(vs_ids, graph->vcount, source_id) || !in_int_array(vs_ids, graph->vcount, target_id)) {
114 | raise_error(2);
115 | }
116 | */
117 |
118 | /* confirm edge is not already in graph */
119 | else if (in_int_array(graph->vs[source_id].out_edges, graph->vs[source_id].out_degree, target_id)) {
120 | raise_error(3);
121 | }
122 | else {
123 |
124 | /* memory reallocation flags */
125 | bool reallocate_out_edges = true;
126 | bool reallocate_in_edges = true;
127 |
128 | /* allocate memory for source_id out_edge record if needed */
129 | if (graph->vs[source_id].out_degree == 0) {
130 | graph->vs[source_id].out_edges = malloc(sizeof(long long int));
131 | reallocate_out_edges = false;
132 | }
133 |
134 | /* allocate memory for target_id in_edge record if needed */
135 | if (graph->vs[target_id].in_degree == 0) {
136 | graph->vs[target_id].in_edges = malloc(sizeof(long long int));
137 | reallocate_in_edges = false;
138 | }
139 |
140 | /* check for problems */
141 | if (graph->vs[target_id].in_edges==NULL || graph->vs[source_id].out_edges==NULL) {
142 | raise_error(0);
143 | }
144 |
145 | /* append the new source_id and target_id */
146 | add_to_int_array(&graph->vs[source_id].out_edges, graph->vs[source_id].out_degree, target_id, reallocate_out_edges);
147 | add_to_int_array(&graph->vs[target_id].in_edges, graph->vs[target_id].in_degree, source_id, reallocate_in_edges);
148 |
149 | /* increment degree counts */
150 | graph->vs[source_id].out_degree++;
151 | graph->vs[target_id].in_degree++;
152 |
153 | /* increment graph ecount */
154 | graph->ecount++;
155 |
156 | }
157 | }
158 |
159 | /**
160 | * \function free_graph
161 | * \brief Free memory taken by a graph.
162 | *
163 | * \param graph The input graph.
164 | */
165 | void free_graph(Graph *graph) {
166 | for (long long int i = 0; i < graph->vcount; i++) {
167 | if (graph->vs[i].in_degree > 0) free(graph->vs[i].in_edges);
168 | if (graph->vs[i].out_degree > 0) free(graph->vs[i].out_edges);
169 | }
170 | free(graph->vs);
171 | }
172 |
--------------------------------------------------------------------------------
/src/main.c:
--------------------------------------------------------------------------------
1 | /*
2 | cdindex library.
3 | Copyright (C) 2017 Russell J. Funk
4 |
5 | This program is free software: you can redistribute it and/or modify
6 | it under the terms of the GNU General Public License as published by
7 | the Free Software Foundation, either version 3 of the License, or
8 | (at your option) any later version.
9 |
10 | This program is distributed in the hope that it will be useful,
11 | but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | GNU General Public License for more details.
14 |
15 | You should have received a copy of the GNU General Public License
16 | along with this program. If not, see .
17 | */
18 |
19 | #include
20 | #include
21 | #include
22 | #include "cdindex.h"
23 |
24 | int main() {
25 |
26 | /* initialize graph components */
27 | int VERTICES = 11;
28 | int EDGES = 13;
29 |
30 | /* dummy data */
31 | long long int raw_vertices_time[] = {694245600,
32 | 694245600,
33 | 725868000,
34 | 725868000,
35 | 788940000,
36 | 852098400,
37 | 883634400,
38 | 915170400,
39 | 915170400,
40 | 883634400,
41 | 852098400};
42 | long long int raw_edges[13][2] = {{4,2},
43 | {4,0},
44 | {4,1},
45 | {4,3},
46 | {5,2},
47 | {6,2},
48 | {6,4},
49 | {7,4},
50 | {8,4},
51 | {9,4},
52 | {9,1},
53 | {9,3},
54 | {10,4}};
55 |
56 | /* create an empty graph */
57 | CREATE_GRAPH(g);
58 |
59 | /* add vertices to the graph */
60 | for (int i = 0; i < VERTICES; i++) {
61 | add_vertex(&g, i, raw_vertices_time[i]);
62 | }
63 |
64 | /* add edges to the graph */
65 | for (int p = 0; p < EDGES; p++) {
66 | add_edge(&g, raw_edges[p][0], raw_edges[p][1]);
67 | }
68 |
69 | /* test and report sanity */
70 | printf("Testing graph sanity: %s\n", is_graph_sane(&g) ? "PASS" : "FAIL");
71 |
72 | /* compute cdindex measure */
73 | printf("CD index: %f\n", cdindex(&g, 4, 157852800));
74 |
75 | /* compute mcdindex measure */
76 | printf("mCD index: %f\n", mcdindex(&g, 4, 157852800));
77 |
78 | /* free memory use by the graph */
79 | free_graph(&g);
80 |
81 | return 0;
82 | }
83 |
--------------------------------------------------------------------------------
/src/utility.c:
--------------------------------------------------------------------------------
1 | /*
2 | cdindex library.
3 | Copyright (C) 2017 Russell J. Funk
4 |
5 | This program is free software: you can redistribute it and/or modify
6 | it under the terms of the GNU General Public License as published by
7 | the Free Software Foundation, either version 3 of the License, or
8 | (at your option) any later version.
9 |
10 | This program is distributed in the hope that it will be useful,
11 | but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | GNU General Public License for more details.
14 |
15 | You should have received a copy of the GNU General Public License
16 | along with this program. If not, see .
17 | */
18 |
19 | #include
20 | #include
21 | #include
22 |
23 | /**
24 | * \function raise_error
25 | * \brief Raise an error.
26 | *
27 | * \param code The error code.
28 | */
29 | void raise_error(int code) {
30 | const char *error[4];
31 | error[0] = "Problem (re)allocating memory";
32 | error[1] = "Vertex ids must be added sequentially from 0";
33 | error[2] = "One or more vertices are not in the graph";
34 | error[3] = "The edge being added is already in the graph";
35 |
36 | fprintf(stderr, "%s\n", error[code]);
37 | exit(EXIT_FAILURE);
38 | }
39 |
40 | /**
41 | * \function in_int_array
42 | * \brief See if an integer is in an integer array.
43 | *
44 | * \param array The input array.
45 | * \param sizeof_array The size of the input array.
46 | * \param value The value to look for in the input array.
47 | *
48 | * \return Whether value is in the array.
49 | */
50 | bool in_int_array(long long int *array, long long int sizeof_array, long long int value) {
51 | bool in_array = false;
52 | for (long long int i = 0; i < sizeof_array; i++) {
53 | if (array[i] == value) {
54 | in_array = true;
55 | }
56 | }
57 | return in_array;
58 | }
59 |
60 | /**
61 | * \function add_to_int_array
62 | * \brief Add an integer to an integer array.
63 | *
64 | * \param array The input array.
65 | * \param sizeof_array The size of the input array.
66 | * \param value The value to add to the array.
67 | * \param add_memory Whether to add memory to the array.
68 | */
69 | void add_to_int_array(long long int **array, long long int sizeof_array, long long int value, bool add_memory) {
70 | long long int *tmp;
71 | if (add_memory) {
72 | tmp = realloc(*array, (sizeof_array + 1) * sizeof(long long int));
73 | if (tmp==NULL) {
74 | raise_error(0);
75 | }
76 | else {
77 | *array = tmp;
78 | }
79 | }
80 | (*array)[sizeof_array] = value;
81 | }
82 |
--------------------------------------------------------------------------------
/tests.py:
--------------------------------------------------------------------------------
1 | #!/usr/local/bin/python
2 | # -*- coding: utf-8 -*-
3 |
4 | """tests.py: This script runs simple tests on the cdindex module."""
5 |
6 | __author__ = "Russell J. Funk"
7 | __copyright__ = "Copyright (C) 2024"
8 |
9 | # built in modules
10 | import datetime
11 |
12 | # custom modules
13 | import cdindex.cdindex
14 | import cdindex._cdindex as _cdindex
15 |
16 | # dummy vertices for c module tests
17 | ctimes = (694224000,
18 | 694224000,
19 | 725846400,
20 | 725846400,
21 | 788918400,
22 | 852098400,
23 | 883612800,
24 | 915148800,
25 | 915148800,
26 | 883612800,
27 | 852076800)
28 |
29 | # dummy edges for c module tests
30 | cedges = ((4,2),
31 | (4,0),
32 | (4,1),
33 | (4,3),
34 | (5,2),
35 | (6,2),
36 | (6,4),
37 | (7,4),
38 | (8,4),
39 | (9,4),
40 | (9,1),
41 | (9,3),
42 | (10,4))
43 |
44 | # dummy vertices for python module tests
45 | pyvertices= [{"name": "0Z", "time": datetime.datetime(1992, 1, 1)},
46 | {"name": "1Z", "time": datetime.datetime(1992, 1, 1)},
47 | {"name": "2Z", "time": datetime.datetime(1993, 1, 1)},
48 | {"name": "3Z", "time": datetime.datetime(1993, 1, 1)},
49 | {"name": "4Z", "time": datetime.datetime(1995, 1, 1)},
50 | {"name": "5Z", "time": datetime.datetime(1997, 1, 1)},
51 | {"name": "6Z", "time": datetime.datetime(1998, 1, 1)},
52 | {"name": "7Z", "time": datetime.datetime(1999, 1, 1)},
53 | {"name": "8Z", "time": datetime.datetime(1999, 1, 1)},
54 | {"name": "9Z", "time": datetime.datetime(1998, 1, 1)},
55 | {"name": "10Z", "time": datetime.datetime(1997, 1, 1)}]
56 |
57 | # dummy edges for python module tests
58 | pyedges = [{"source": "4Z", "target": "2Z"},
59 | {"source": "4Z", "target": "0Z"},
60 | {"source": "4Z", "target": "1Z"},
61 | {"source": "4Z", "target": "3Z"},
62 | {"source": "5Z", "target": "2Z"},
63 | {"source": "6Z", "target": "2Z"},
64 | {"source": "6Z", "target": "4Z"},
65 | {"source": "7Z", "target": "4Z"},
66 | {"source": "8Z", "target": "4Z"},
67 | {"source": "9Z", "target": "4Z"},
68 | {"source": "9Z", "target": "1Z"},
69 | {"source": "9Z", "target": "3Z"},
70 | {"source": "10Z", "target": "4Z"}]
71 |
72 | # test time
73 | TEST_TIME = 157852800
74 | TEST_TIME_PY = datetime.timedelta(days=1827)
75 |
76 | # tests for the c extension
77 | def c_tests():
78 | """Run tests for c extension."""
79 |
80 | # create graph
81 | graph = _cdindex.Graph()
82 |
83 | # add vertices
84 | for id, time in enumerate(ctimes):
85 | _cdindex.add_vertex(graph, id, time)
86 |
87 | # add edges
88 | for source, target in cedges:
89 | _cdindex.add_edge(graph, source, target)
90 |
91 | # examine the graph
92 | print("Vertices in graph: %s" % (_cdindex.get_vcount(graph)))
93 | print("Edges in graph: %s" % (_cdindex.get_ecount(graph)))
94 | print("Graph sanity: %s" % (_cdindex._is_graph_sane(graph)))
95 |
96 | # examine properties of a vertices
97 | for vertex in _cdindex.get_vertices(graph):
98 | print("%s: %-5s | %s: %-15s %s: %-10s %s: %-10s %s at %s: %-20s %s at %s: %-20s %s: %-20s %s: %-20s"
99 | % ("vertex", vertex,
100 | "timestamp", _cdindex.get_vertex_timestamp(graph, vertex),
101 | "in degree", _cdindex.get_vertex_in_degree(graph, vertex),
102 | "out degree", _cdindex.get_vertex_out_degree(graph, vertex),
103 | "cd index", TEST_TIME, _cdindex.cdindex(graph, vertex, TEST_TIME),
104 | "mcd index", TEST_TIME, _cdindex.mcdindex(graph, vertex, TEST_TIME),
105 | "in edges", _cdindex.get_vertex_in_edges(graph, vertex),
106 | "out edges", _cdindex.get_vertex_out_edges(graph, vertex)))
107 |
108 | # tests for the python module
109 | def py_tests():
110 | """Run tests for python module."""
111 |
112 | # create graph
113 | graph = cdindex.Graph()
114 |
115 | # add vertices
116 | for vertex in pyvertices:
117 | graph.add_vertex(vertex["name"], cdindex.timestamp_from_datetime(vertex["time"]))
118 |
119 | # add edges
120 | for edge in pyedges:
121 | graph.add_edge(edge["source"], edge["target"])
122 |
123 | # examine the graph
124 | print("Vertices in graph: %s" % (graph.vcount()))
125 | print("Edges in graph: %s" % (graph.ecount()))
126 | print("Graph sanity: %s" % (graph._is_graph_sane()))
127 |
128 | # examine properties of a vertices
129 | for vertex in graph.vertices():
130 | print("%s: %-5s | %s: %-15s %s: %-10s %s: %-10s %s at %s: %-20s %s at %s: %-20s %s: %-35s %s: %-35s"
131 | % ("vertex", vertex,
132 | "timestamp", graph.timestamp(vertex),
133 | "in degree", graph.in_degree(vertex),
134 | "out degree", graph.out_degree(vertex),
135 | "cd index", TEST_TIME_PY, graph.cdindex(vertex, int(TEST_TIME_PY.total_seconds())),
136 | "mcd index", TEST_TIME_PY, graph.mcdindex(vertex, int(TEST_TIME_PY.total_seconds())),
137 | "in edges", graph.in_edges(vertex),
138 | "out edges", graph.out_edges(vertex)))
139 |
140 | def main():
141 |
142 | # run c tests
143 | c_tests()
144 |
145 | # run python tests
146 | py_tests()
147 |
148 | # generate random graph
149 | g = cdindex.RandomGraph(generations=(2,3,4,5,6,7,7,9), edge_fraction=1)
150 |
151 | # print some information
152 | print(g.ecount())
153 | print(g.vcount())
154 |
155 | if __name__ == "__main__":
156 | main()
157 |
--------------------------------------------------------------------------------