Preparing next minor patch

codemeta.json

@@ -93,7 +93,7 @@
         }
     ],
     "softwareRequirements": "https://raw.githubusercontent.com/KnowledgeCaptureAndDiscovery/somef/refs/heads/master/pyproject.toml",
-    "version": "0.11.1",
+    "version": "0.11.2",
     "developmentStatus": "active",
     "issueTracker": "https://github.com/KnowledgeCaptureAndDiscovery/somef/issues",
     "@type": "SoftwareSourceCode"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "somef"
-version = "0.11.1"
+version = "0.11.2"
 description = "SOftware Metadata Extraction Framework: A tool for automatically extracting relevant software metadata from a source code repository (README, package files, etc)."
 authors = ["Daniel Garijo <daniel.garijo@upm.es>"]
 readme = "README.md"

src/somef/__init__.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "0.11.1"
+__version__ = "0.11.2"

src/somef/export/json_export.py

@@ -443,7 +443,16 @@ def format_date(date_string):
                 is_bibtex = False
 
                 if constants.PROP_FORMAT in cit[constants.PROP_RESULT] and cit[constants.PROP_RESULT][constants.PROP_FORMAT] == "cff":
-                    yaml_content = yaml.safe_load(cit[constants.PROP_RESULT]["value"])
+                    # yaml_content = yaml.safe_load(cit[constants.PROP_RESULT]["value"])
+                    cff_value = cit[constants.PROP_RESULT]["value"]
+                    try:
+                        yaml_content = yaml.safe_load(cff_value) 
+                    except Exception:
+                        # Remove HTML tags that can break YAML parsing
+                        # ej:" <a href="..."> " has unescaped quotes
+                        cleaned = re.sub(constants.REGEXP_CLEAN_HTML_TAGS, '', cff_value)
+                        yaml_content = yaml.safe_load(cleaned)
+
                     preferred_citation = yaml_content.get("preferred-citation", {})
                     doi = yaml_content.get("doi") or preferred_citation.get("doi")
                     identifiers = yaml_content.get("identifiers", [])
@@ -514,6 +523,8 @@ def format_date(date_string):
                             "@type": "Organization",
                             "name": name
                         }
+                    else:
+                        continue
 
                     if family_name and given_name and orcid:
                         key = (family_name.lower(), given_name.lower())

src/somef/process_files.py

@@ -611,7 +611,11 @@ def get_file_content_or_link(repo_type, file_path, owner, repo_name, repo_defaul
                 try:
                     yaml_content = yaml.safe_load(file_text)
                 except Exception:
-                    yaml_content = None
+                    cleaned = re.sub(constants.REGEXP_CLEAN_HTML_TAGS, '', file_text)
+                    try:
+                        yaml_content = yaml.safe_load(cleaned)
+                    except Exception:
+                        yaml_content = None
 
                 if yaml_content:
                     license_value = yaml_content.get("license")

src/somef/test/test_JSON_export.py

@@ -1144,4 +1144,34 @@ def test_issue_533_choosealicense_badge(self):
 
         os.remove(output_path)
 
-
+    def test_issue_1050(self):
+        """citation.cff yaml parsing with unescaped quotes in abstract should not crash"""
+        somef_cli.run_cli(threshold=0.8,
+                        ignore_classifiers=False,
+                        repo_url=None,
+                        local_repo=test_data_repositories + "nemo",
+                        output=test_data_path + "test_issue_1050.json",
+                        pretty=True,
+                        readme_only=False)
+
+
+        with open(test_data_path + "test_issue_1050.json") as f:
+            json_content = json.load(f)
+
+        cff_entries = [
+            c for c in json_content.get(constants.CAT_CITATION, [])
+            if "CITATION.cff" in c.get("source", "")
+        ]
+        assert len(cff_entries) > 0, "CITATION.cff not found in citations"
+
+        cff_entry = json_content[constants.CAT_CITATION][0]["result"]
+        assert cff_entry.get("title") == "NEMO: A Stellar Dynamics Toolbox"
+        assert cff_entry.get("type") == "SoftwareApplication"
+
+        cff_authors = cff_entry.get("author", [])
+        assert len(cff_authors) == 3
+        orcid_urls = [a.get("url") for a in cff_authors]
+        assert all(u and u.startswith("https://orcid.org/") for u in orcid_urls)
+
+        os.remove(test_data_path + "test_issue_1050.json")
+

src/somef/test/test_codemeta_export.py

@@ -968,6 +968,29 @@ def test_issue_1025_orcid(self):
         os.remove(output_path)
 
 
+    def test_codemeta_nemo_cff_issue_1050(self):
+        """CITATION.cff with HTML in abstract exports with unescaped quotes correctly to codemeta"""
+        output_path = test_data_path + 'test_codemeta_nemo.json'
+        somef_cli.run_cli(threshold=0.8,
+                        ignore_classifiers=False,
+                        repo_url=None,
+                        local_repo=test_data_repositories + "nemo",
+                        output=None,
+                        codemeta_out=output_path,
+                        pretty=True,
+                        readme_only=False)
+
+        with open(output_path) as f:
+            json_content = json.load(f)
+
+        credit_text = json_content.get(constants.CAT_CODEMETA_CREDITTEXT, [])
+        assert len(credit_text) > 0
+        assert any("NEMO" in ct.upper() for ct in credit_text)
+        assert any("BARNES" in ct.upper() for ct in credit_text)
+
+        os.remove(output_path)
+
+
     @classmethod
     def tearDownClass(cls):
         """delete temp file JSON just if all the test pass"""

src/somef/test/test_data/repositories/nemo/CITATION.cff

@@ -0,0 +1,23 @@
+cff-version: 1.2.0
+message: "Please cite the following works when using this software: https://ui.adsabs.harvard.edu/abs/1995ASPC...77..398T"
+authors:
+- family-names: Barnes
+  given-names: Joshua
+  orcid: https://orcid.org/0000-0002-3371-1082
+- family-names: Hut
+  given-names: Piet
+  orcid:  https://orcid.org/0000-0001-7565-5843
+- family-names: Teuben
+  given-names: Peter
+  orcid: https://orcid.org/0000-0003-1774-3436
+title: "NEMO: A Stellar Dynamics Toolbox"
+version: 4.4.0
+date-released: 2022-11-01
+identifiers:
+ - type: "ascl-id"
+   value: "1010.051"
+ - type: "doi"
+   value: PLACEHOLDER
+ - type: "bibcode"
+   value: "2010ascl.soft10051B"
+abstract: "NEMO is an extendible  Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (<a href="http://ascl.net/1102.027">ascl:1102.027</a>) for the version that Barnes maintains."

src/somef/test/test_data/repositories/nemo/README.md

@@ -0,0 +1,185 @@
+![A Real Bar](docs/figures/realbar1.png)
+
+NEMO is a toolbox for stellar dynamics, particle simulations, stellar orbits,
+image processing and tabular data manipulation. Documentation is maintained
+in the github pages, https://teuben.github.io/nemo , and a manual in
+https://astronemo.readthedocs.io
+
+Unless otherwise specified, all code has been written by a human.
+
+
+## History
+
+This is the 4th major release of NEMO,  and although data are compatible
+with earlier releases, old source code may need to be tweaked a
+bit to compile and link in the newer releases. Some compatibility with ZENO
+is also advertised. A brief history of NEMO:
+
+   * NEMO V1:	IAS release (Barnes, Hut & Teuben, 1987)
+   * NEMO V2:	UMD release (Teuben, 1994)
+   * NEMO V3:	UMD release (Teuben, 2001) in CVS, w/ autoconf, manybody, starlab and partiview
+   * NEMO V4:   UMD/ESO release (2017) now maintained in github
+
+A related package, ZENO, was spun off NEMO V1, and is maintained by Josh Barnes. 
+Other packages that geneologically came after NEMO are StarLab, ACS and AMUSE
+(see also https://ascl.net for code references):
+
+   * NEMO:      ascl:1010.051
+   * ZENO:      ascl:1102.027 (normally installed in $NEMO/usr/zeno)
+   * STARLAB:   ascl:1010.076 (optionally installed in $NEMO/local/starlab)
+   * ACS:       [https://artcompsci.org](https://web.archive.org/web/20240206050455/http://www.artcompsci.org)
+   * AMUSE:     ascl:1107.007
+
+## Optional Packages
+
+
+	 PGPLOT:    ascl:1103.002
+	 CFITSIO:   ascl:1010.001
+	 WCSLIB:    ascl:1108.003
+	 glnemo2:   ascl:1110.008
+	 gyrfalcON: ascl:1402.031 (included with NEMO)
+	 HDF4
+	 HDF5       https://www.hdfgroup.org
+	 netcdf4
+	 gsl
+	 plplot
+	 unsio
+	 uns_project
+	 wcstools
+
+Tools you will need to have pre-installed: the C/C++/Fortran
+compilers, (t)csh, and git.  For graphics it's probably useful to have
+pgplot, but the default ps driver works fine just to get started.
+We are looking for more portable full graphics, as an alternative
+to pgplot.
+
+The files in $NEMO/src/scripts/linux describe the actual package
+names for different linux distros that should lead to success.
+
+
+## Installation
+
+There are a few different ways to install NEMO.
+We cover an annotated example in this
+[bash notebook](scripts/notebooks/installing.ipynb)
+or the deprecated
+[bash notebook](example.ipynb).
+
+And here is a simple
+example that works most of the time on most Linux (including WSL) distros:
+
+         git clone https://github.com/teuben/nemo
+         cd nemo
+         ./configure --with-yapp=pgplot
+         make build check bench5
+         source nemo_start.sh
+
+If you plan to modify code and submit pull requests, the github CLI is recommended,
+though you can of course also clone the upstream manually
+(see also [CONTRIBUTING.md](CONTRIBUTING.md)):
+
+         gh repo fork https://github.com/teuben/nemo
+
+After installation, rebuilding NEMO to ensure you have all updates can be done as follows:
+
+         cd $NEMO
+         git pull
+         make rebuild
+
+this may be overkill for some situations, but gets the job done.
+
+### python
+
+There is now a small python component to NEMO, in the **nemopy** module.
+
+         cd $NEMO
+         pip install -e .
+
+but this will depend on the details of how your python environment exists (virtual, conda etc.).
+We leave this to the user.
+
+## Examples		 
+
+If you want to quickly see something work, here are the commands to
+make a classic 1911 Plummer sphere of just 10 particles, print the positions, plot
+the positions and view the contents of its binary file:
+
+         mkplummer p10.dat 10
+         snapprint p10.dat
+         snapplot p10.dat
+         tsf p10.dat
+
+and here is an example of creating the 4 major data objects on the fly in NEMO
+(table, snapshot, image, orbit), showing off the command line interface and
+use of Unix pipes, with a dash denoting the piped file:
+
+         tabgen -  | tabplot -
+         mkplummer - 100 | snapplot - 
+         ccdgen out=- object=gauss spar=1,20 size=128 | ccdplot - 
+         mkorbit - 0 1 0  0.4 0 0 potname=plummer | orbint - - nsteps=1000 dt=0.05 | orbplot - 
+
+or graphically showing the pipes through arrows:
+
+```mermaid
+   graph LR;
+   A[tabgen]-->B[tabplot]
+
+   C[mkplummer]-->D[snapplot]
+
+   E[ccdgen]-->F[ccdplot]
+
+   G[mkorbit]-->H[orbint]
+   H-->I[orbplot]
+```
+
+There are more examples of scripts and figures in
+https://teuben.github.io/nemo/examples/ 
+and an example ipython notebook is shown here
+https://github.com/teuben/nemo/blob/master/nemo_start_example.ipynb
+for something completely different.
+
+A reproducable example is given in this notebook. To run this from the command line
+and print the phase space coordinates of the first particle, use this:
+
+      mkplummer - 10 seed=123| snapprint -  | head -1
+      ### nemo Debug Info: x y z vx vy vz 
+      -0.609486 -0.221687 -0.450963 -0.0766784 -0.209397 0.396561 
+
+
+## Documentation and Help
+
+There are several additional entry points if you are starting out with NEMO,
+between them there is unavoidable duplication, but here they are:
+
+* readthedocs: https://astronemo.readthedocs.io/en/latest/
+* github pages: https://teuben.github.io/nemo  (yes, these are the 1990s style webpages we used to maintain)
+* all unix style man pages for all levels: https://teuben.github.io/nemo/man_html/index1.html
+* the nemo man page https://teuben.github.io/nemo/man_html/nemo.1.html
+* software carpentry: https://teuben.github.io/nemo-lesson 
+* AAS 443 [iPoster](https://aas243-aas.ipostersessions.com/?s=85-F6-32-6F-83-00-4E-79-54-7F-C0-25-77-D7-0D-7B)
+* an installation example in bash jupyter notebook style: https://github.com/teuben/nemo/blob/master/scripts/notebooks/installing.ipynb
+* contributing to NEMO: https://github.com/teuben/nemo/blob/master/CONTRIBUTING.md
+
+## Citation
+
+Please use the following citation if you use NEMO in your work
+
+
+     @INPROCEEDINGS{1995ASPC...77..398T,
+            author = {{Teuben}, P.},
+             title = "{The Stellar Dynamics Toolbox NEMO}",
+         booktitle = {Astronomical Data Analysis Software and Systems IV},
+              year = 1995,
+            editor = {{Shaw}, R.~A. and {Payne}, H.~E. and {Hayes}, J.~J.~E.},
+            series = {Astronomical Society of the Pacific Conference Series},
+            volume = {77},
+             month = jan,
+             pages = {398},
+            adsurl = {https://ui.adsabs.harvard.edu/abs/1995ASPC...77..398T},
+           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+     }
+
+
+![A Real Bar](docs/figures/realbar1.png)
+
+[taken from this example script](https://teuben.github.io/nemo/examples/realbar.html)

src/somef/utils/constants.py

@@ -106,6 +106,8 @@
 # Detect copyright information in license files. 
 REGEXP_COPYRIGHT = r"copyright\s*(?:\(c\)|©|\(C\))?\s*\{?(\d{4}(?:-\d{4})?)\}?\s*\{?([^\n}]+)\}?"
 
+REGEXP_CLEAN_HTML_TAGS = r'<[^>]+>'
+
 LICENSES_DICT = {
     "Apache License 2.0": {"regex": REGEXP_APACHE, "spdx_id": "Apache-2.0"},
     "GNU General Public License v3.0": {"regex": REGEXP_GPL3, "spdx_id": "GPL-3.0"},