brsynth · guillaume-gricourt · Mar 17, 2023 · Feb 23, 2023 · Feb 23, 2023 · Feb 23, 2023
diff --git a/.github/CODE_OF_CONDUCT.rst b/.github/CODE_OF_CONDUCT.rst
@@ -0,0 +1,49 @@
+Code of Conduct
+===============
+
+- Be friendly and patient
+- Be respectful
+- Be welcoming
+- Be considerate
+- Focus on what's best for the community
+- Gracefully accept constructive criticism
+- Show courtesy and respect towards other community members
+- Be respectful of different viewpoints and experiences
+- Use welcoming and inclusive language
+
+Reporting an issue
+------------------
+If you see a violation of the code of conduct, please report it to anyone belonging to the [BioRetroSynth organization](https://github.com/orgs/brsynth/people).  If the person who is harassing you belongs to the team, he will recuse himself from handling your incident. We will respond as promptly as we can.
+To protect volunteers from abuse and burnout, we reserve the right to reject any report we believe to have been made with the deliberate intention of deceiving or misleading the committee.
+
+Enforcement
+-----------
+Upon receiving a report, the Maintainer core team will meet privately to discuss
+the matter and determine the best course of action.
+
+Possible responses may include:
+
+- taking no further action (if we determine no violation occurred)
+- a private reprimand from the core members to the individual(s) involved. In
+  this case, a core member will deliver that reprimand via email, copying the
+  rest of the core.
+- a public reprimand. In this case a core member will deliver the reprimand via
+  the same channel as the violation occurred (e.g., via comment on PR or issue)
+- an imposed vacation (e.g., asking the individual to refrain from participating
+  for a week). A core member will deliver a request for the individual to take
+  such a "vacation" voluntarily, but if they don't disagree then a temporary
+  ban may be imposed.
+- a permanent or temporary ban from the repository
+
+Once a resolution is agreed upon, but before it is enacted, the core will
+contact the original reporter and discuss the resolution and will note any
+feedback for the record, but is not obligated to act on such feedback.
+
+The core will never publicly discuss the issue; any public statements will be
+made by core members.
+
+If the incident involves a core member, the core member must recuse themselves
+from the response process.
+
+This policy was modified from
+`django project <https://www.djangoproject.com/conduct/enforcement-manual>`_
diff --git a/.github/CONTRIBUTING.rst b/.github/CONTRIBUTING.rst
@@ -0,0 +1,65 @@
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+Ways you can help
+-----------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/brsynth/neo4jsbml/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version, versions of Neo4j and SBML specification.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with
+"enhancement" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Same as Implement Features
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/brsynth/neo4jsbml/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* This will hopefully become a community-driven project and contributions
+  are welcome :)
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring.
+2. Passing ``pytest``
+
+   .. code-block:: console
+
+        $ python -m pytest
+
+3. Passing `super-linter <https://github.com/marketplace/actions/super-linter>`_
+
+This policy was modified from
+`planemo project <https://github.com/galaxyproject/planemo/blob/master/CONTRIBUTING.rst>`_
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -42,11 +42,14 @@ jobs:
           fetch-depth: 0
       - name: 'Check file present'
         run: |
-          [[ -f CHANGELOG.md ]] || touch CHANGELOG.md
+          [[ -f CHANGELOG.rst ]] || touch CHANGELOG.rst
       - uses: ruby/setup-ruby@v1
         with:
           ruby-version: 3 # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+      - uses: docker://pandoc/core:2.9
+        with:
+          args: -o CHANGELOG.md CHANGELOG.rst
       - name: 'Generate CHANGELOG'
         env:
           CHANGELOG_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -56,11 +59,14 @@ jobs:
           PROJECT=$(echo "$GITHUB_REPOSITORY" | sed -e 's/\// /g' | awk '{print $2}')
           echo "$USER $PROJECT"
           github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
+      - uses: docker://pandoc/core:2.9
+        with:
+          args: -o CHANGELOG.rst CHANGELOG.md
       - name: 'Upload Artifact Changelog'
         uses: actions/upload-artifact@v3
         with:
           name: changelog-artifact
-          path: CHANGELOG.md
+          path: CHANGELOG.rst
           retention-days: 1
 
   Version:

diff --git a/.gitignore b/.gitignore
@@ -24,3 +24,6 @@ debug
 papier
 cmd.sh
 *.xml
+# Docs
+_build
+generated
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,27 @@
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+   os: ubuntu-22.04
+   tools:
+     python: "3.10"
+     # You can also specify other tool versions:
+     # nodejs: "16"
+     # rust: "1.55"
+     # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
+
+formats:
+  - pdf
+  - epub
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -0,0 +1,55 @@
+Changelog
+=========
+
+`0.9.1 <https://github.com/brsynth/neo4jsbml/tree/0.9.1>`__ (2023-02-21)
+------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.0...0.9.1>`__
+
+.. _section-1:
+
+`0.9.0 <https://github.com/brsynth/neo4jsbml/tree/0.9.0>`__ (2023-01-27)
+------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/0.8.3...0.9.0>`__
+
+**Merged pull requests:**
+
+-  chore(deps): bump actions/upload-artifact from 2 to 3
+   `#4 <https://github.com/brsynth/neo4jsbml/pull/4>`__
+   (`dependabot[bot] <https://github.com/apps/dependabot>`__)
+
+.. _section-2:
+
+`0.8.3 <https://github.com/brsynth/neo4jsbml/tree/0.8.3>`__ (2023-01-16)
+------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/0.8.0...0.8.3>`__
+
+.. _section-3:
+
+`0.8.0 <https://github.com/brsynth/neo4jsbml/tree/0.8.0>`__ (2023-01-16)
+------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/710ac296807b62182b8280c407d990537bacdce7...0.8.0>`__
+
+**Implemented enhancements:**
+
+-  Provide config file
+   `#2 <https://github.com/brsynth/neo4jsbml/pull/2>`__
+   (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
+
+**Merged pull requests:**
+
+-  Feat modelisation pathway
+   `#3 <https://github.com/brsynth/neo4jsbml/pull/3>`__
+   (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
+-  Package `#1 <https://github.com/brsynth/neo4jsbml/pull/1>`__
+   (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
+
+\* *This Changelog was automatically generated by*
+`github_changelog_generator <https://github.com/github-changelog-generator/github-changelog-generator>`__
diff --git a/README.md b/README.md
@@ -19,24 +19,25 @@ pip install --no-deps .
 ### Step 1
 
 Create a schema with [arrows](https://arrows.app) like:  
-![schema](tests/dataset/PathwayModelisation-1.0.0.png "Schema SBML")
+![schema](docs/_static/PathwayModelisation-1.0.0.arrows.png "Schema SBML")  
 Rules:
 * Nodes are labelled based on SBML object name as defined in the [SBML specification](https://sbml.org)
 * Properties are labelled based on SBML object properties as defined the [SBML specification](https://sbml.org)
 
 ### Step 2
 
-Export your schema at the JSON format.
+Export your schema at the JSON format.  
+![schema](docs/_static/arrows.dwl.png "Download JSON")
 
 ### Step 3
 
 Import your data with `neo4jsbml` into Neo4j.  
-* Use either a configuration file `ini`, an example is provided in the `template` directory or individual parameters
+* Use either a configuration file `ini` or individual parameters
 * Password needs to be store in a file for safety security
-* Pass a `tag` to identify the model loaded into the database
+* If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
 
 ```sh
-python -m neo4jsbml \
+neo4jsbml \
     # Database parameters
     --input-protocol-str ["neo4j", "bolt"] \
     --input-url-str "localhost" \
@@ -52,9 +53,3 @@ python -m neo4jsbml \
     --input-tag-str "" \
     --input-modelisation-json <file>
 ```
-
-## Test
-
-```sh
-python -m pytest
-```
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/1.2-0-2.png b/docs/_static/1.2-0-2.png
diff --git a/docs/_static/2.2-0-2.png b/docs/_static/2.2-0-2.png
diff --git a/docs/_static/3.2-0-2.png b/docs/_static/3.2-0-2.png
diff --git a/docs/_static/PathwayModelisation-1.0.0.arrows.png b/docs/_static/PathwayModelisation-1.0.0.arrows.png
diff --git a/tests/dataset/PathwayModelisation-1.0.0.png → docs/_static/PathwayModelisation-1.0.0.png b/tests/dataset/PathwayModelisation-1.0.0.png → docs/_static/PathwayModelisation-1.0.0.png
diff --git a/docs/_static/PathwayModelisation-2.0.2.png b/docs/_static/PathwayModelisation-2.0.2.png
diff --git a/docs/_static/arrows.dwl.png b/docs/_static/arrows.dwl.png
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -0,0 +1 @@
+.. include:: ../CHANGELOG.rst
diff --git a/docs/conduct.rst b/docs/conduct.rst
@@ -0,0 +1 @@
+.. include:: ../.github/CODE_OF_CONDUCT.rst
-Original file line number
+Diff line change
@@ Expand Up / @@ -24,3 +24,6 @@ debug @@
     papier
     cmd.sh
     *.xml
+    # Docs
+    _build
+    generated