├── .gitignore
├── FOSS4Spec.xlsx
├── FOSS4Spec_2025-05-12.xlsx
├── FOSS4Spectroscopy.Rmd
├── Include
    ├── Table1.png
    └── sorttable.js
├── LICENSE
├── README.md
├── Render.R
├── Utilities
    ├── dereplicate_repos.R
    ├── final_manual_check.R
    ├── review_candidates.R
    └── run_searches.R
├── docs
    └── index.html
└── ~$FOSS4Spec.xlsx


/.gitignore:
--------------------------------------------------------------------------------
1 | *.Rhistory
2 | .DS_Store
3 | .Rapp.history
4 | .Rproj.user/
5 | *~
6 | Links404.csv
7 | DateReport.csv
8 | Searches/
9 | 


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/FOSS4Spec.xlsx:
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/FOSS4Spec_2025-05-12.xlsx:
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/FOSS4Spectroscopy.Rmd:
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  1 | ---
  2 | title: FOSS For Spectroscopy
  3 | author: Bryan A. Hanson, DePauw University
  4 | date: >-
  5 |   `r paste(format(Sys.time(),
  6 |   format = "%Y-%m-%d %H:%M", tz = "GMT"), "UTC")`
  7 | output:
  8 |   html_document:
  9 |     theme: united
 10 | ---
 11 | 
 12 | <script data-goatcounter="https://foss4spec.goatcounter.com/count"
 13 |         async src="//gc.zgo.at/count.js"></script>
 14 |         
 15 | <!-- Following code to keep printed version cleaner; see https://stackoverflow.com/a/24467913/633251  -->
 16 | <style type="text/css" media="print">
 17 | a:link:after, a:visited:after {
 18 |   content: normal !important;
 19 | }
 20 | </style>
 21 | 
 22 | 
 23 | <!-- See https://kryogenix.org/code/browser/sorttable/ -->
 24 | <script src="Include/sorttable.js"></script>
 25 | 
 26 | The following table collects information about free and open source software ([FOSS](https://en.wikipedia.org/wiki/Free_and_open-source_software)) for spectroscopy.  All information is taken from the respective websites and/or repositories.  Some projects have been described in publications.  If so, we try to provide a link, but the document may be behind a paywall.  This [blog post](https://chemospec.org/posts/2021-04-19-Search-GH-Topics/2021-04-19-Search-GH-Topics.html) give some details about how  we find interesting repositories.
 27 | 
 28 | Unless otherwise noted, the software mentioned here:
 29 | 
 30 | * Is suitable for one or more of the following techniques: NMR, IR, Raman, ESR/EPR, fluorescence, XRF, LIBS and UV-Vis.
 31 | * Mass *spectrometry* software is not included (see the work by Stanstrup just below).
 32 | * Software for MRI is not included.
 33 | * Software for remote sensing is generally not included, though some projects involving hyperspectral imaging are included.
 34 | * While some folks publish open source add-ons for `Matlab`, `Matlab` is not open source and projects written in `Matlab` are not included.
 35 | 
 36 | Some other places to look:
 37 | 
 38 | * [Stanstrup *et al.*](https://www.mdpi.com/2218-1989/9/10/200) have published a comprehensive paper describing the `R` packages suitable for use in metabolomics, which partially overlaps with the information here. The authors have also created a dynamic [document](https://rformassspectrometry.github.io/metaRbolomics-book/) with the same information and more.
 39 | * [awesome-spectra](https://github.com/erwanp/awesome-spectra) is a page somewhat in the spirit of the work here, but apparently depends on authors to add their own material, and is missing some key entries (e.g. no NMR packages).
 40 | * [All Things Raman](https://github.com/allthingsraman) is a curated collection of software for Raman spectroscopy.
 41 | * The [CRAN Task View for Chemometrics & Computational Physics](https://cran.r-project.org/web/views/ChemPhys.html) includes some `R` packages listed here as well as related software.
 42 | 
 43 | #### How Does One Choose a Package?
 44 | 
 45 | *The projects listed here have been lightly vetted and the process is imperfect!* If a project looks incomplete, is a class project, or I can't tell what it does, it's not included!* Of course, if you feel I have not included your package in error, feel free to request its inclusion.  With that in mind, there are still many packages to consider.  As a general guide, the excellent checklist provided by [Lortie *et al.*](https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5970) is included here for your consideration.
 46 | 
 47 | <img src="Include/Table1.png" alt="Lortie Table 1" width="50%">
 48 | 
 49 | ```{r setupR, echo = FALSE, results = "hide"}
 50 | # Clean up the workspace but keep the local token, if present
 51 | # This is necessary for the local build
 52 | keep <- "github_token"
 53 | rm(list = ls()[!(ls() %in% keep)])
 54 | 
 55 | suppressPackageStartupMessages(library("knitr"))
 56 | suppressPackageStartupMessages(library("gt"))
 57 | suppressPackageStartupMessages(library("readxl"))
 58 | suppressPackageStartupMessages(library("httr"))
 59 | suppressPackageStartupMessages(library("lubridate"))
 60 | suppressPackageStartupMessages(library("jsonlite"))
 61 | suppressPackageStartupMessages(library("rvest")) #???
 62 | suppressPackageStartupMessages(library("stringr"))
 63 | suppressPackageStartupMessages(library("xml2"))
 64 | suppressPackageStartupMessages(library("webu"))
 65 | 
 66 | opts_chunk$set(echo = FALSE)
 67 | 
 68 | set_config(timeout(40)) # httr setting for GET calls (default 13)
 69 | cnt <- 0L # counter for the number of GET calls to Github
 70 | username <- "bryanhanson"
 71 | ```
 72 | 
 73 | 
 74 | ```{r readDB}
 75 | # Please edit FOSS4Spec.xlsx to add information or make corrections.
 76 | # Please follow the conventions of existing entries for consistency.
 77 | # Remember the table in the web page is sortable so consistency in
 78 | # description and focus is especially important for users to obtain
 79 | # useful information easily.
 80 | 
 81 | DF <- as.data.frame(read_excel("FOSS4Spec.xlsx", na = "NA"))
 82 | # shorten names for less typing
 83 | names(DF) <- c("pkgname", "desc", "lang", "focus", "repo", "web", "pub", "maint", "maint_email", "author_email")
 84 | DF <- DF[order(DF$pkgname),]
 85 | ```
 86 | 
 87 | ```{r token}
 88 | junk <- check_for_github_token(github_token)
 89 | ```
 90 | 
 91 | ```{r verifyURLs}
 92 | # This takes some time!
 93 | ne <- nrow(DF) # number of entries
 94 | 
 95 | # Check all URLs, if the site is down handle so table always looks good.
 96 | # Site URL might also just be missing from table, handle this too.
 97 | webLink <- rep(FALSE, ne) # If TRUE, there is a link in the input table
 98 | repoLink <- rep(FALSE, ne)
 99 | pubLink <- rep(FALSE, ne)
100 | 
101 | webOK <- rep(FALSE, ne) # If TRUE, URL was reachable
102 | repoOK <- rep(FALSE, ne)
103 | pubOK <- rep(FALSE, ne)
104 | 
105 | # These are used for internal reporting
106 | # If TRUE, URL was given but not reachable
107 | badWeb <- rep(FALSE, ne)
108 | badRepo <- rep(FALSE, ne)
109 | badPub <- rep(FALSE, ne)
110 | 
111 | for (i in 1:ne) {
112 |   if (!is.na(DF$web[i])) {
113 |     webOK[i] <- good_url(DF$web[i])
114 |     webLink[i] <- TRUE
115 |     if (webLink[i] != webOK[i]) badWeb[i] <- TRUE
116 |   }
117 | 
118 |   if (!is.na(DF$repo[i])) {
119 |     repoOK[i] <- good_url(DF$repo[i])
120 |     repoLink[i] <- TRUE
121 |     if (repoLink[i] != repoOK[i]) badRepo[i] <- TRUE
122 |   }
123 | 
124 |   if (!is.na(DF$pub[i])) {
125 |     pubOK[i] <- good_url(DF$pub[i])
126 |     pubLink[i] <- TRUE
127 |     if (pubLink[i] != pubOK[i]) badPub[i] <- TRUE
128 |   }
129 | }
130 | # If URLs are bad they will still be added to the table as hyperlinks, but
131 | # those links will give status 404.
132 | # Write a report so maintainers can check & fix if it's on our end
133 | LinkReport <- data.frame(name = DF$pkgname, webLink, webOK, repoLink, repoOK, pubLink, pubOK, stringsAsFactors = FALSE)
134 | keep <- badPub | badRepo | badWeb
135 | LinkReport <- LinkReport[keep,]
136 | if (nrow(LinkReport) > 0) write.csv(LinkReport, row.names = FALSE, file = "Reports/Links404.csv")
137 | ```
138 | 
139 | ```{r checkUpdateDate, warning = FALSE}
140 | # Use the info from checking URLs above
141 | webDate <- as.POSIXct(rep(NA, ne)) # see stackoverflow.com/a/33002710/633251
142 | commitDate <- as.POSIXct(rep(NA, ne))
143 | issueDate <- as.POSIXct(rep(NA, ne))
144 | updateDate <- as.POSIXct(rep(NA, ne))
145 | 
146 | repoType <- rep("xx", ne)
147 | repoType[grepl("github\\.com", DF$repo)] <- "gh"
148 | 
149 | for (i in 1:ne) {
150 | 
151 |   if (webOK[i]) {
152 |     ans <- find_page_date(flatten_web_page(DF$web[i]))
153 |     if (!is.na(ans)) webDate[i] <- ans
154 |   }
155 | 
156 |   if (repoOK[i]) {
157 |     if (repoType[i] == "gh") {
158 |       # NA returned when repo path bad
159 |       tmp <- get_github_dates(DF$repo[i], "commits")
160 |       cnt <- cnt + 1
161 |       if (!is.na(tmp)) commitDate[i] <- ymd(tmp)
162 |       tmp <- get_github_dates(DF$repo[i], "issues")
163 |       cnt <- cnt + 1
164 |       if (!is.na(tmp)) issueDate[i] <- ymd(tmp)
165 |     }
166 |   }
167 | 
168 |   # updateDate will be the most recent of webDate, issueDate, commitDate
169 |   # If all are NA, a warning is issued so to avoid that do:
170 |   if (is.na(webDate[i]) & is.na(commitDate[i]) & is.na(issueDate[i])) next
171 |   updateDate[i] <- max(webDate[i], commitDate[i], issueDate[i], na.rm = TRUE)
172 | }
173 | updateDate <- date(updateDate) # -> ymd
174 | 
175 | # Write a report
176 | DateReport <- data.frame(name = DF$pkgname, webDate, commitDate, issueDate, updateDate, stringsAsFactors = FALSE)
177 | write.csv(DateReport, row.names = FALSE, file = "Reports/DateReport.csv")
178 | ```
179 | 
180 | ```{r createNamelink}
181 | # Additional processing of the input values
182 | # Combine name, website and pub as available to create hyperlink
183 | # If website is missing, use repo instead (otherwise one must edit the original table more)
184 | namelink <- DF$pkgname # There must be at least a pkgname in the input table
185 | for (i in 1:ne) {
186 |   if (!is.na(DF$web[i])) {
187 |     namelink[i] <- paste("[", DF$pkgname[i], "](", DF$web[i], ")", sep = "")
188 |   }
189 |   if (is.na(DF$web[i])) {
190 |     if (!is.na(DF$repo[i])) {
191 |       namelink[i] <- paste("[", DF$pkgname[i], "](", DF$repo[i], ")", sep = "")
192 |     }
193 |   }
194 |   if (!is.na(DF$pub[i])) {
195 |     namelink[i] <- paste(namelink[i], " ([pub](", DF$pub[i], "))", sep = "")
196 |   }
197 | }
198 | ```
199 | 
200 | ```{r createTable}
201 | DF2 <- data.frame(namelink, DF$desc, DF$lang, DF$focus, updateDate, stringsAsFactors = FALSE)
202 | names(DF2) <- c("Name", "Description", "Lang", "Focus", "Status")
203 | ```
204 | 
205 | <hr>
206 | 
207 | * *Click on a header to sort the table ("Focus" may be a good starting point)*
208 | * [Abbreviations](#abbreviations) & terms below the table
209 | * The table currently has `r nrow(DF2)` entries; the majority are `R` (`r length(DF2$Lang[DF2$Lang == "R"])`) or `Python` (`r length(DF2$Lang[DF2$Lang == "Python"])`).
210 | 
211 | ```{r printTable, results = "asis"}
212 | DF2 |>
213 |   gt()|>
214 |   opt_stylize(style = 1) |>
215 |   fmt_markdown()
216 | ```
217 | 
218 | Additions or corrections?  Please [file an issue](https://github.com/bryanhanson/FOSS4Spectroscopy/issues) with the necessary information or submit a pull request at the [repo](https://github.com/bryanhanson/FOSS4Spectroscopy).
219 | 
220 | ##### Status Column: {#status}
221 | 
222 | The status column in the table gives the date of the most recent:
223 | 
224 | * commit to a repository,
225 | * activity on an issue filed in a repository,
226 | * web site update, or
227 | * submission to an archival network such as CRAN or PyPI
228 | 
229 | as a proxy for regular maintenance, at the time this page was updated.  Keep in mind that some software is fairly mature and thus an older status date does not necessarily mean the software is not maintained.  Follow the links to the websites for more details.
230 | 
231 | *The status date is found by automatic checking of sites with valid links.  Commits and issues are only checked for Github sites, via the Github API. Web site updates are found using a simple search for common date formats and may be inaccurate. Keep in mind the most recent activity may be on any branch in a repo, and may be newer than any official releases.*[^1]
232 | 
233 | ##### Abbreviations & Terms: {#abbreviations}
234 | 
235 | * __CRAN:__ [Comprehensive R Archival Network](https://cran.r-project.org/)
236 | * __EDA:__ Exploratory data analysis (unsupervised chemometrics)
237 | * __Focus:__ The type of spectroscopy the software is focused on. Keep in mind that software designed with a given spectroscopy in mind may still work with other types of spectroscopic data.
238 | * __Language:__ Most software is built on several languages. In the table, "lang" refers to the primary language used to create the software.
239 | * __PyPI:__ [Python Package Index](https://pypi.org/)
240 | * __Python:__ Multipurpose programming language [details](https://www.python.org/about/)
241 | * __R:__ A software environment for statistical computing and graphics [details, platforms](https://www.r-project.org/)
242 | 
243 | 
244 | [^1]: We made `r cnt` inquiries to Github to produce this report.
245 | 


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/Include/sorttable.js:
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  1 | /*
  2 |   SortTable
  3 |   version 2
  4 |   7th April 2007
  5 |   Stuart Langridge, http://www.kryogenix.org/code/browser/sorttable/
  6 | 
  7 |   Instructions:
  8 |   Download this file
  9 |   Add <script src="sorttable.js"></script> to your HTML
 10 |   Add class="sortable" to any table you'd like to make sortable
 11 |   Click on the headers to sort
 12 | 
 13 |   Thanks to many, many people for contributions and suggestions.
 14 |   Licenced as X11: http://www.kryogenix.org/code/browser/licence.html
 15 |   This basically means: do what you want with it.
 16 | */
 17 | 
 18 | 
 19 | var stIsIE = /*@cc_on!@*/false;
 20 | 
 21 | sorttable = {
 22 |   init: function() {
 23 |     // quit if this function has already been called
 24 |     if (arguments.callee.done) return;
 25 |     // flag this function so we don't do the same thing twice
 26 |     arguments.callee.done = true;
 27 |     // kill the timer
 28 |     if (_timer) clearInterval(_timer);
 29 | 
 30 |     if (!document.createElement || !document.getElementsByTagName) return;
 31 | 
 32 |     sorttable.DATE_RE = /^(\d\d?)[\/\.-](\d\d?)[\/\.-]((\d\d)?\d\d)$/;
 33 | 
 34 |     forEach(document.getElementsByTagName('table'), function(table) {
 35 |       if (table.className.search(/\bsortable\b/) != -1) {
 36 |         sorttable.makeSortable(table);
 37 |       }
 38 |     });
 39 | 
 40 |   },
 41 | 
 42 |   makeSortable: function(table) {
 43 |     if (table.getElementsByTagName('thead').length == 0) {
 44 |       // table doesn't have a tHead. Since it should have, create one and
 45 |       // put the first table row in it.
 46 |       the = document.createElement('thead');
 47 |       the.appendChild(table.rows[0]);
 48 |       table.insertBefore(the,table.firstChild);
 49 |     }
 50 |     // Safari doesn't support table.tHead, sigh
 51 |     if (table.tHead == null) table.tHead = table.getElementsByTagName('thead')[0];
 52 | 
 53 |     if (table.tHead.rows.length != 1) return; // can't cope with two header rows
 54 | 
 55 |     // Sorttable v1 put rows with a class of "sortbottom" at the bottom (as
 56 |     // "total" rows, for example). This is B&R, since what you're supposed
 57 |     // to do is put them in a tfoot. So, if there are sortbottom rows,
 58 |     // for backwards compatibility, move them to tfoot (creating it if needed).
 59 |     sortbottomrows = [];
 60 |     for (var i=0; i<table.rows.length; i++) {
 61 |       if (table.rows[i].className.search(/\bsortbottom\b/) != -1) {
 62 |         sortbottomrows[sortbottomrows.length] = table.rows[i];
 63 |       }
 64 |     }
 65 |     if (sortbottomrows) {
 66 |       if (table.tFoot == null) {
 67 |         // table doesn't have a tfoot. Create one.
 68 |         tfo = document.createElement('tfoot');
 69 |         table.appendChild(tfo);
 70 |       }
 71 |       for (var i=0; i<sortbottomrows.length; i++) {
 72 |         tfo.appendChild(sortbottomrows[i]);
 73 |       }
 74 |       delete sortbottomrows;
 75 |     }
 76 | 
 77 |     // work through each column and calculate its type
 78 |     headrow = table.tHead.rows[0].cells;
 79 |     for (var i=0; i<headrow.length; i++) {
 80 |       // manually override the type with a sorttable_type attribute
 81 |       if (!headrow[i].className.match(/\bsorttable_nosort\b/)) { // skip this col
 82 |         mtch = headrow[i].className.match(/\bsorttable_([a-z0-9]+)\b/);
 83 |         if (mtch) { override = mtch[1]; }
 84 | 	      if (mtch && typeof sorttable["sort_"+override] == 'function') {
 85 | 	        headrow[i].sorttable_sortfunction = sorttable["sort_"+override];
 86 | 	      } else {
 87 | 	        headrow[i].sorttable_sortfunction = sorttable.guessType(table,i);
 88 | 	      }
 89 | 	      // make it clickable to sort
 90 | 	      headrow[i].sorttable_columnindex = i;
 91 | 	      headrow[i].sorttable_tbody = table.tBodies[0];
 92 | 	      dean_addEvent(headrow[i],"click", sorttable.innerSortFunction = function(e) {
 93 | 
 94 |           if (this.className.search(/\bsorttable_sorted\b/) != -1) {
 95 |             // if we're already sorted by this column, just
 96 |             // reverse the table, which is quicker
 97 |             sorttable.reverse(this.sorttable_tbody);
 98 |             this.className = this.className.replace('sorttable_sorted',
 99 |                                                     'sorttable_sorted_reverse');
100 |             this.removeChild(document.getElementById('sorttable_sortfwdind'));
101 |             sortrevind = document.createElement('span');
102 |             sortrevind.id = "sorttable_sortrevind";
103 |             sortrevind.innerHTML = stIsIE ? '&nbsp<font face="webdings">5</font>' : '&nbsp;&#x25B4;';
104 |             this.appendChild(sortrevind);
105 |             return;
106 |           }
107 |           if (this.className.search(/\bsorttable_sorted_reverse\b/) != -1) {
108 |             // if we're already sorted by this column in reverse, just
109 |             // re-reverse the table, which is quicker
110 |             sorttable.reverse(this.sorttable_tbody);
111 |             this.className = this.className.replace('sorttable_sorted_reverse',
112 |                                                     'sorttable_sorted');
113 |             this.removeChild(document.getElementById('sorttable_sortrevind'));
114 |             sortfwdind = document.createElement('span');
115 |             sortfwdind.id = "sorttable_sortfwdind";
116 |             sortfwdind.innerHTML = stIsIE ? '&nbsp<font face="webdings">6</font>' : '&nbsp;&#x25BE;';
117 |             this.appendChild(sortfwdind);
118 |             return;
119 |           }
120 | 
121 |           // remove sorttable_sorted classes
122 |           theadrow = this.parentNode;
123 |           forEach(theadrow.childNodes, function(cell) {
124 |             if (cell.nodeType == 1) { // an element
125 |               cell.className = cell.className.replace('sorttable_sorted_reverse','');
126 |               cell.className = cell.className.replace('sorttable_sorted','');
127 |             }
128 |           });
129 |           sortfwdind = document.getElementById('sorttable_sortfwdind');
130 |           if (sortfwdind) { sortfwdind.parentNode.removeChild(sortfwdind); }
131 |           sortrevind = document.getElementById('sorttable_sortrevind');
132 |           if (sortrevind) { sortrevind.parentNode.removeChild(sortrevind); }
133 | 
134 |           this.className += ' sorttable_sorted';
135 |           sortfwdind = document.createElement('span');
136 |           sortfwdind.id = "sorttable_sortfwdind";
137 |           sortfwdind.innerHTML = stIsIE ? '&nbsp<font face="webdings">6</font>' : '&nbsp;&#x25BE;';
138 |           this.appendChild(sortfwdind);
139 | 
140 | 	        // build an array to sort. This is a Schwartzian transform thing,
141 | 	        // i.e., we "decorate" each row with the actual sort key,
142 | 	        // sort based on the sort keys, and then put the rows back in order
143 | 	        // which is a lot faster because you only do getInnerText once per row
144 | 	        row_array = [];
145 | 	        col = this.sorttable_columnindex;
146 | 	        rows = this.sorttable_tbody.rows;
147 | 	        for (var j=0; j<rows.length; j++) {
148 | 	          row_array[row_array.length] = [sorttable.getInnerText(rows[j].cells[col]), rows[j]];
149 | 	        }
150 | 	        /* If you want a stable sort, uncomment the following line */
151 | 	        //sorttable.shaker_sort(row_array, this.sorttable_sortfunction);
152 | 	        /* and comment out this one */
153 | 	        row_array.sort(this.sorttable_sortfunction);
154 | 
155 | 	        tb = this.sorttable_tbody;
156 | 	        for (var j=0; j<row_array.length; j++) {
157 | 	          tb.appendChild(row_array[j][1]);
158 | 	        }
159 | 
160 | 	        delete row_array;
161 | 	      });
162 | 	    }
163 |     }
164 |   },
165 | 
166 |   guessType: function(table, column) {
167 |     // guess the type of a column based on its first non-blank row
168 |     sortfn = sorttable.sort_alpha;
169 |     for (var i=0; i<table.tBodies[0].rows.length; i++) {
170 |       text = sorttable.getInnerText(table.tBodies[0].rows[i].cells[column]);
171 |       if (text != '') {
172 |         if (text.match(/^-?[£$¤]?[\d,.]+%?$/)) {
173 |           return sorttable.sort_numeric;
174 |         }
175 |         // check for a date: dd/mm/yyyy or dd/mm/yy
176 |         // can have / or . or - as separator
177 |         // can be mm/dd as well
178 |         possdate = text.match(sorttable.DATE_RE)
179 |         if (possdate) {
180 |           // looks like a date
181 |           first = parseInt(possdate[1]);
182 |           second = parseInt(possdate[2]);
183 |           if (first > 12) {
184 |             // definitely dd/mm
185 |             return sorttable.sort_ddmm;
186 |           } else if (second > 12) {
187 |             return sorttable.sort_mmdd;
188 |           } else {
189 |             // looks like a date, but we can't tell which, so assume
190 |             // that it's dd/mm (English imperialism!) and keep looking
191 |             sortfn = sorttable.sort_ddmm;
192 |           }
193 |         }
194 |       }
195 |     }
196 |     return sortfn;
197 |   },
198 | 
199 |   getInnerText: function(node) {
200 |     // gets the text we want to use for sorting for a cell.
201 |     // strips leading and trailing whitespace.
202 |     // this is *not* a generic getInnerText function; it's special to sorttable.
203 |     // for example, you can override the cell text with a customkey attribute.
204 |     // it also gets .value for <input> fields.
205 | 
206 |     if (!node) return "";
207 | 
208 |     hasInputs = (typeof node.getElementsByTagName == 'function') &&
209 |                  node.getElementsByTagName('input').length;
210 | 
211 |     if (node.getAttribute("sorttable_customkey") != null) {
212 |       return node.getAttribute("sorttable_customkey");
213 |     }
214 |     else if (typeof node.textContent != 'undefined' && !hasInputs) {
215 |       return node.textContent.replace(/^\s+|\s+$/g, '');
216 |     }
217 |     else if (typeof node.innerText != 'undefined' && !hasInputs) {
218 |       return node.innerText.replace(/^\s+|\s+$/g, '');
219 |     }
220 |     else if (typeof node.text != 'undefined' && !hasInputs) {
221 |       return node.text.replace(/^\s+|\s+$/g, '');
222 |     }
223 |     else {
224 |       switch (node.nodeType) {
225 |         case 3:
226 |           if (node.nodeName.toLowerCase() == 'input') {
227 |             return node.value.replace(/^\s+|\s+$/g, '');
228 |           }
229 |         case 4:
230 |           return node.nodeValue.replace(/^\s+|\s+$/g, '');
231 |           break;
232 |         case 1:
233 |         case 11:
234 |           var innerText = '';
235 |           for (var i = 0; i < node.childNodes.length; i++) {
236 |             innerText += sorttable.getInnerText(node.childNodes[i]);
237 |           }
238 |           return innerText.replace(/^\s+|\s+$/g, '');
239 |           break;
240 |         default:
241 |           return '';
242 |       }
243 |     }
244 |   },
245 | 
246 |   reverse: function(tbody) {
247 |     // reverse the rows in a tbody
248 |     newrows = [];
249 |     for (var i=0; i<tbody.rows.length; i++) {
250 |       newrows[newrows.length] = tbody.rows[i];
251 |     }
252 |     for (var i=newrows.length-1; i>=0; i--) {
253 |        tbody.appendChild(newrows[i]);
254 |     }
255 |     delete newrows;
256 |   },
257 | 
258 |   /* sort functions
259 |      each sort function takes two parameters, a and b
260 |      you are comparing a[0] and b[0] */
261 |   sort_numeric: function(a,b) {
262 |     aa = parseFloat(a[0].replace(/[^0-9.-]/g,''));
263 |     if (isNaN(aa)) aa = 0;
264 |     bb = parseFloat(b[0].replace(/[^0-9.-]/g,''));
265 |     if (isNaN(bb)) bb = 0;
266 |     return aa-bb;
267 |   },
268 |   sort_alpha: function(a,b) {
269 |     if (a[0]==b[0]) return 0;
270 |     if (a[0]<b[0]) return -1;
271 |     return 1;
272 |   },
273 |   sort_ddmm: function(a,b) {
274 |     mtch = a[0].match(sorttable.DATE_RE);
275 |     y = mtch[3]; m = mtch[2]; d = mtch[1];
276 |     if (m.length == 1) m = '0'+m;
277 |     if (d.length == 1) d = '0'+d;
278 |     dt1 = y+m+d;
279 |     mtch = b[0].match(sorttable.DATE_RE);
280 |     y = mtch[3]; m = mtch[2]; d = mtch[1];
281 |     if (m.length == 1) m = '0'+m;
282 |     if (d.length == 1) d = '0'+d;
283 |     dt2 = y+m+d;
284 |     if (dt1==dt2) return 0;
285 |     if (dt1<dt2) return -1;
286 |     return 1;
287 |   },
288 |   sort_mmdd: function(a,b) {
289 |     mtch = a[0].match(sorttable.DATE_RE);
290 |     y = mtch[3]; d = mtch[2]; m = mtch[1];
291 |     if (m.length == 1) m = '0'+m;
292 |     if (d.length == 1) d = '0'+d;
293 |     dt1 = y+m+d;
294 |     mtch = b[0].match(sorttable.DATE_RE);
295 |     y = mtch[3]; d = mtch[2]; m = mtch[1];
296 |     if (m.length == 1) m = '0'+m;
297 |     if (d.length == 1) d = '0'+d;
298 |     dt2 = y+m+d;
299 |     if (dt1==dt2) return 0;
300 |     if (dt1<dt2) return -1;
301 |     return 1;
302 |   },
303 | 
304 |   shaker_sort: function(list, comp_func) {
305 |     // A stable sort function to allow multi-level sorting of data
306 |     // see: http://en.wikipedia.org/wiki/Cocktail_sort
307 |     // thanks to Joseph Nahmias
308 |     var b = 0;
309 |     var t = list.length - 1;
310 |     var swap = true;
311 | 
312 |     while(swap) {
313 |         swap = false;
314 |         for(var i = b; i < t; ++i) {
315 |             if ( comp_func(list[i], list[i+1]) > 0 ) {
316 |                 var q = list[i]; list[i] = list[i+1]; list[i+1] = q;
317 |                 swap = true;
318 |             }
319 |         } // for
320 |         t--;
321 | 
322 |         if (!swap) break;
323 | 
324 |         for(var i = t; i > b; --i) {
325 |             if ( comp_func(list[i], list[i-1]) < 0 ) {
326 |                 var q = list[i]; list[i] = list[i-1]; list[i-1] = q;
327 |                 swap = true;
328 |             }
329 |         } // for
330 |         b++;
331 | 
332 |     } // while(swap)
333 |   }
334 | }
335 | 
336 | /* ******************************************************************
337 |    Supporting functions: bundled here to avoid depending on a library
338 |    ****************************************************************** */
339 | 
340 | // Dean Edwards/Matthias Miller/John Resig
341 | 
342 | /* for Mozilla/Opera9 */
343 | if (document.addEventListener) {
344 |     document.addEventListener("DOMContentLoaded", sorttable.init, false);
345 | }
346 | 
347 | /* for Internet Explorer */
348 | /*@cc_on @*/
349 | /*@if (@_win32)
350 |     document.write("<script id=__ie_onload defer src=javascript:void(0)><\/script>");
351 |     var script = document.getElementById("__ie_onload");
352 |     script.onreadystatechange = function() {
353 |         if (this.readyState == "complete") {
354 |             sorttable.init(); // call the onload handler
355 |         }
356 |     };
357 | /*@end @*/
358 | 
359 | /* for Safari */
360 | if (/WebKit/i.test(navigator.userAgent)) { // sniff
361 |     var _timer = setInterval(function() {
362 |         if (/loaded|complete/.test(document.readyState)) {
363 |             sorttable.init(); // call the onload handler
364 |         }
365 |     }, 10);
366 | }
367 | 
368 | /* for other browsers */
369 | window.onload = sorttable.init;
370 | 
371 | // written by Dean Edwards, 2005
372 | // with input from Tino Zijdel, Matthias Miller, Diego Perini
373 | 
374 | // http://dean.edwards.name/weblog/2005/10/add-event/
375 | 
376 | function dean_addEvent(element, type, handler) {
377 | 	if (element.addEventListener) {
378 | 		element.addEventListener(type, handler, false);
379 | 	} else {
380 | 		// assign each event handler a unique ID
381 | 		if (!handler.$$guid) handler.$$guid = dean_addEvent.guid++;
382 | 		// create a hash table of event types for the element
383 | 		if (!element.events) element.events = {};
384 | 		// create a hash table of event handlers for each element/event pair
385 | 		var handlers = element.events[type];
386 | 		if (!handlers) {
387 | 			handlers = element.events[type] = {};
388 | 			// store the existing event handler (if there is one)
389 | 			if (element["on" + type]) {
390 | 				handlers[0] = element["on" + type];
391 | 			}
392 | 		}
393 | 		// store the event handler in the hash table
394 | 		handlers[handler.$$guid] = handler;
395 | 		// assign a global event handler to do all the work
396 | 		element["on" + type] = handleEvent;
397 | 	}
398 | };
399 | // a counter used to create unique IDs
400 | dean_addEvent.guid = 1;
401 | 
402 | function removeEvent(element, type, handler) {
403 | 	if (element.removeEventListener) {
404 | 		element.removeEventListener(type, handler, false);
405 | 	} else {
406 | 		// delete the event handler from the hash table
407 | 		if (element.events && element.events[type]) {
408 | 			delete element.events[type][handler.$$guid];
409 | 		}
410 | 	}
411 | };
412 | 
413 | function handleEvent(event) {
414 | 	var returnValue = true;
415 | 	// grab the event object (IE uses a global event object)
416 | 	event = event || fixEvent(((this.ownerDocument || this.document || this).parentWindow || window).event);
417 | 	// get a reference to the hash table of event handlers
418 | 	var handlers = this.events[event.type];
419 | 	// execute each event handler
420 | 	for (var i in handlers) {
421 | 		this.$$handleEvent = handlers[i];
422 | 		if (this.$$handleEvent(event) === false) {
423 | 			returnValue = false;
424 | 		}
425 | 	}
426 | 	return returnValue;
427 | };
428 | 
429 | function fixEvent(event) {
430 | 	// add W3C standard event methods
431 | 	event.preventDefault = fixEvent.preventDefault;
432 | 	event.stopPropagation = fixEvent.stopPropagation;
433 | 	return event;
434 | };
435 | fixEvent.preventDefault = function() {
436 | 	this.returnValue = false;
437 | };
438 | fixEvent.stopPropagation = function() {
439 |   this.cancelBubble = true;
440 | }
441 | 
442 | // Dean's forEach: http://dean.edwards.name/base/forEach.js
443 | /*
444 | 	forEach, version 1.0
445 | 	Copyright 2006, Dean Edwards
446 | 	License: http://www.opensource.org/licenses/mit-license.php
447 | */
448 | 
449 | // array-like enumeration
450 | if (!Array.forEach) { // mozilla already supports this
451 | 	Array.forEach = function(array, block, context) {
452 | 		for (var i = 0; i < array.length; i++) {
453 | 			block.call(context, array[i], i, array);
454 | 		}
455 | 	};
456 | }
457 | 
458 | // generic enumeration
459 | Function.prototype.forEach = function(object, block, context) {
460 | 	for (var key in object) {
461 | 		if (typeof this.prototype[key] == "undefined") {
462 | 			block.call(context, object[key], key, object);
463 | 		}
464 | 	}
465 | };
466 | 
467 | // character enumeration
468 | String.forEach = function(string, block, context) {
469 | 	Array.forEach(string.split(""), function(chr, index) {
470 | 		block.call(context, chr, index, string);
471 | 	});
472 | };
473 | 
474 | // globally resolve forEach enumeration
475 | var forEach = function(object, block, context) {
476 | 	if (object) {
477 | 		var resolve = Object; // default
478 | 		if (object instanceof Function) {
479 | 			// functions have a "length" property
480 | 			resolve = Function;
481 | 		} else if (object.forEach instanceof Function) {
482 | 			// the object implements a custom forEach method so use that
483 | 			object.forEach(block, context);
484 | 			return;
485 | 		} else if (typeof object == "string") {
486 | 			// the object is a string
487 | 			resolve = String;
488 | 		} else if (typeof object.length == "number") {
489 | 			// the object is array-like
490 | 			resolve = Array;
491 | 		}
492 | 		resolve.forEach(object, block, context);
493 | 	}
494 | };
495 | 


--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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  2 |                        Version 3, 29 June 2007
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674 | <https://www.gnu.org/licenses/why-not-lgpl.html>.
675 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | This repo drives the creation of the [FOSS for Spectroscopy](https://bryanhanson.github.io/FOSS4Spectroscopy/) page.
 2 | 
 3 | ## I have info to contribute, but I'm not familiar with Github pull requests
 4 | 
 5 | If you have information to add to the table, or corrections, and are not familiar with pull requests on `Github`, [file an issue](https://github.com/bryanhanson/FOSS4Spectroscopy/issues) and we'll gladly update the site with your information.
 6 | 
 7 | ## I have info to contribute, and I know how to do a pull request on Github
 8 | 
 9 | If you wish to contribute to improving the content, appearance or performance of the table, please file a pull request.
10 | 
11 | * `FOSS4Spec.xlsx` contains the raw data -- if you have additions or corrections you can add/fix them there. I can then process the page to update it, or you can do it yourself (next point).
12 | * `FOSS4Spectroscopy.Rmd` contains the code to process the input and check the links, if you'd like to improve or enhance the automation/display.  The `Rmd` file relies on a package `webu` which can be found [here](https://github.com/bryanhanson/webu) and is not on CRAN.
13 | 
14 | ## Background
15 | 
16 | See this [blog post](https://chemospec.org/posts/2021-04-19-Search-GH-Topics/2021-04-19-Search-GH-Topics.html) for details about searching for spectroscopy packages automatically to find the raw material that goes into this site. When local changes are pushed, items in the `/docs` folder are deployed to the `gh-pages` site where the general public views the page.  
17 | 
18 | 


--------------------------------------------------------------------------------
/Render.R:
--------------------------------------------------------------------------------
1 | 
2 | # Process the Rmd
3 | # Be sure to run the GH authorization if working locally.
4 | 
5 | library("rmarkdown")
6 | render("FOSS4Spectroscopy.Rmd", output_file = "docs/index.html")
7 | 
8 | 


--------------------------------------------------------------------------------
/Utilities/dereplicate_repos.R:
--------------------------------------------------------------------------------
 1 | #'
 2 | #' Dereplicate Search Results
 3 | #'
 4 | #' Remove repos found by a topic search if we already have them.
 5 | #' Should be run in a dedicated temporary directory containing the
 6 | #' search results.
 7 | #'
 8 | #' @param in_dir Character.  Directory containing file(s) with extension `.xlsx`.
 9 | #'        These files contain the new/fresh search results.
10 | #' @param ref_file Character.  Path to a `.xlsx` file containing already identified
11 | #'        repos of interest. 
12 | #' @param out_file Character. Path to write out results.
13 | #'
14 | 
15 | dereplicate_repos <- function(in_dir, ref_file, out_file) {
16 | 
17 |   # remove the out_file file from a previous run if it is present
18 |   if (file.exists(out_file)) file.remove(out_file)
19 |   
20 |   # read in the reference file
21 |   ref <- as.data.frame(readxl::read_xlsx(ref_file))
22 |   cat("The reference file contains", nrow(ref), "entries\n")
23 | 
24 |   # get the files with new results & merge them
25 |   new_files <- list.files(in_dir, pattern = "\\.xlsx", full.names = TRUE)
26 |   for (i in 1:length(new_files)) {
27 |     new <- as.data.frame(readxl::read_xlsx(new_files[i]))
28 |     cat("Result file", new_files[i], "has", nrow(new), "entries\n")
29 |     if (i == 1L) glob <- new
30 |     if (i > 1L) glob <- merge(glob, new, all = TRUE)
31 |   }
32 |   
33 |   cat("After merging the new files we have", nrow(glob), "entries\n")
34 |   
35 |   # merge the new with the existing results
36 |   glob <- merge(ref, glob, all = TRUE)
37 |   cat("After merging the new files with the existing results we have", nrow(glob), "entries\n")
38 |   
39 |   # do some clean up
40 |   glob <- glob[order(glob$name),]
41 |   toss <- which(duplicated(glob$name))
42 |   glob <- glob[-toss,]
43 |   cat("After removing duplicate rows we have", nrow(glob), "entries\n")
44 |   
45 |   # Save results
46 |   WriteXLS::WriteXLS(glob, out_file,
47 |     row.names = FALSE, col.names = TRUE, na = "NA"
48 |   )
49 | 
50 |   invisible(glob)
51 | }
52 | 


--------------------------------------------------------------------------------
/Utilities/final_manual_check.R:
--------------------------------------------------------------------------------
 1 | #
 2 | # Manual, Final Check for Data Quality of FOSS4Spec.xlsx
 3 | #
 4 | library("readxl")
 5 | library("plyr")
 6 | 
 7 | DF <- read_excel("../Searches/FOSS4Spec.xlsx")
 8 | names(DF)
 9 | 
10 | # Check for duplicated entries
11 | # Some pkgs have the same name but different case.
12 | # Some of these are inconsistent cap situations, some are actually 2 different pkgs.
13 | any(duplicated(tolower(DF$name)))
14 | which(duplicated(tolower(DF$name)))
15 | any(duplicated(DF$name))
16 | 
17 | # Check for language misspellings, mis-classifications
18 | count(DF$language)
19 | 
20 | # Check for inconsistencies in focus
21 | unique(DF$focus)
22 | count(DF$focus)
23 | 


--------------------------------------------------------------------------------
/Utilities/review_candidates.R:
--------------------------------------------------------------------------------
 1 | #'
 2 | #' Step through a list of candidate packages in the R console
 3 | #'
 4 | #' An alternative to manual editing of the Excel file
 5 | #'
 6 | library("readxl")
 7 | 
 8 | review_candidates <- function(file) {
 9 |   DF <- as.data.frame(read_excel(file))
10 |   cat("Press ESC to stop reviewing (data is lost!)\n\n")
11 |   toss <- c()
12 |   for (i in 1:nrow(DF)) {
13 |   	print(DF[i,1:2])
14 |   	ans <- readline("Keep this entry? Return = yes, n = no ")
15 |   	if (ans == "n") toss <- c(toss, i)
16 |   }
17 | 
18 |   DF <- DF[-toss,]
19 |   return(DF)
20 | }
21 | 


--------------------------------------------------------------------------------
/Utilities/run_searches.R:
--------------------------------------------------------------------------------
 1 | 
 2 | # Supervising Script to Search Github or PyPi.org Repos for Topics
 3 | 
 4 | library("webu") # ask me if you want this pkg
 5 | library("WriteXLS")
 6 | 
 7 | # Note 1: Searching PyPi.org via the API one needs to use single quoted strings
 8 | # like "'laser induced breakdown spectroscopy'" otherwise each term is searched separately,
 9 | # leading to lots of false positives.  Single quoted strings like this don't work on Github.
10 | 
11 | # Note 2: Searching for just "VIS" or "IR" leads to too many false positives; as it is,
12 | # "NIR" etc gives a lot of false positives dealing with IR remote controllers.
13 | # There are similar problems with "UV" and "UV-VIS"
14 | # Cannot use "LIBS" as it returns 1,000+ results
15 | 
16 | # Note 3: Run this in an empty folder as a place to store the results.
17 | 
18 | # No authentification needed for PyPi
19 | # PyPi search strings
20 | nmr_topics <- c("NMR")
21 | epr_topics <- c("EPR", "ESR")
22 | vis_topics <- c("spectrophotometry")
23 | ir_topics <- c("'FT-IR'", "FTIR")
24 | raman_topics <- c("Raman")
25 | xrf_topics <- c("XRF", "'laser induced breakdown spectroscopy'", "XAS")
26 | all_topics <- c(nmr_topics, epr_topics, vis_topics, ir_topics, raman_topics, xrf_topics)
27 | 
28 | res_pypi <- search_pypi_for_topics(all_topics, browse = FALSE)
29 | res_pypi2 <- res_pypi[!duplicated(res_pypi),]
30 | WriteXLS::WriteXLS(res_pypi2, "pypi_search_results.xlsx", row.names = FALSE, col.names = TRUE, na = "NA")
31 | 
32 | # Be sure to run the GH authorization to get a local token if searching Github.
33 | # See details at ?set_up_github_token
34 | 
35 | # Github search strings
36 | nmr_topics <- c("NMR")
37 | epr_topics <- c("EPR", "ESR")
38 | vis_topics <- c("spectrophotometry")
39 | ir_topics <- c("FT-IR", "FTIR")
40 | raman_topics <- c("Raman")
41 | xrf_topics <- c("XRF", "LIBS", "XAS")
42 | all_topics <- c(nmr_topics, epr_topics, vis_topics, ir_topics, raman_topics, xrf_topics)
43 | 
44 | res_gh <- search_github_for_topics(topics = all_topics, browse = FALSE, username = "bryanhanson", token = github_token)
45 | 
46 | WriteXLS::WriteXLS(res_gh, "gh_search_results.xlsx", row.names = FALSE, col.names = TRUE, na = "NA")
47 | 
48 | 
49 | 
50 | 


--------------------------------------------------------------------------------
/~$FOSS4Spec.xlsx:
--------------------------------------------------------------------------------
1 | BryanH                                                BryanH                                                


--------------------------------------------------------------------------------