Merge branch 'main' into stable

brsynth · Mar 18, 2024 · 264c580 · 264c580
2 parents f65dbd6 + 03bb73a
commit 264c580
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -19,7 +19,7 @@ jobs:
           fetch-depth: 0
       - name: 'Bump version and push tag - dry run'
         id: tag_raw
-        uses: mathieudutour/github-tag-action@v6.1
+        uses: mathieudutour/github-tag-action@v6.2
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           release_branches: stable
@@ -156,7 +156,7 @@ jobs:
           fetch-depth: 0
       - name: 'Bump version and push tag'
         id: tag
-        uses: mathieudutour/github-tag-action@v6.1
+        uses: mathieudutour/github-tag-action@v6.2
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           release_branches: stable
@@ -210,7 +210,7 @@ jobs:
         with:
           name: package-conda-artifact
       - name: 'Create Release'
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ needs.TagRaw.outputs.tag }}
           body: ${{ needs.TagRaw.outputs.changelog }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.12.0](https://github.com/brsynth/neo4jsbml/tree/0.12.0) (2023-10-08)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.11.2...0.12.0)
+
+**Merged pull requests:**
+
+- Take into account `annotation` field [\#15](https://github.com/brsynth/neo4jsbml/pull/15) ([guillaume-gricourt](https://github.com/guillaume-gricourt))
+
 ## [0.11.2](https://github.com/brsynth/neo4jsbml/tree/0.11.2) (2023-10-07)
 
 [Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.11.1...0.11.2)

diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ Import your data with `neo4jsbml` into Neo4j.
 * 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
-neo4jsbml \
+neo4jsbml sbml-to-neo4j \
     # Database parameters
     --input-protocol-str ["neo4j", "neo4j+s", "neo4j+ssc", "bolt", "bolt+s", "bolt+ssc"] \
     --input-url-str "localhost" \

diff --git a/docs/CHANGELOG.data.rst b/docs/CHANGELOG.data.rst
@@ -1,6 +1,20 @@
 Changelog
 =========
 
+`0.12.0 <https://github.com/brsynth/neo4jsbml/tree/0.12.0>`__ (2023-10-08)
+--------------------------------------------------------------------------
+
+`Full
+Changelog <https://github.com/brsynth/neo4jsbml/compare/0.11.2...0.12.0>`__
+
+**Merged pull requests:**
+
+-  Take into account ``annotation`` field
+   `#15 <https://github.com/brsynth/neo4jsbml/pull/15>`__
+   (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
+
+.. _section-1:
+
 `0.11.2 <https://github.com/brsynth/neo4jsbml/tree/0.11.2>`__ (2023-10-07)
 --------------------------------------------------------------------------
 
@@ -19,7 +33,7 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.11.1...0.11.2>`__
    `#11 <https://github.com/brsynth/neo4jsbml/pull/11>`__
    (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
 
-.. _section-1:
+.. _section-2:
 
 `0.11.1 <https://github.com/brsynth/neo4jsbml/tree/0.11.1>`__ (2023-09-22)
 --------------------------------------------------------------------------
@@ -39,7 +53,7 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.11.0...0.11.1>`__
    `#8 <https://github.com/brsynth/neo4jsbml/pull/8>`__
    (`dependabot[bot] <https://github.com/apps/dependabot>`__)
 
-.. _section-2:
+.. _section-3:
 
 `0.11.0 <https://github.com/brsynth/neo4jsbml/tree/0.11.0>`__ (2023-03-28)
 --------------------------------------------------------------------------
@@ -53,15 +67,15 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.10.1...0.11.0>`__
    `#7 <https://github.com/brsynth/neo4jsbml/pull/7>`__
    (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
 
-.. _section-3:
+.. _section-4:
 
 `0.10.1 <https://github.com/brsynth/neo4jsbml/tree/0.10.1>`__ (2023-03-17)
 --------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.10.0...0.10.1>`__
 
-.. _section-4:
+.. _section-5:
 
 `0.10.0 <https://github.com/brsynth/neo4jsbml/tree/0.10.0>`__ (2023-03-17)
 --------------------------------------------------------------------------
@@ -77,23 +91,23 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.2...0.10.0>`__
 -  Read the docs `#5 <https://github.com/brsynth/neo4jsbml/pull/5>`__
    (`guillaume-gricourt <https://github.com/guillaume-gricourt>`__)
 
-.. _section-5:
+.. _section-6:
 
 `0.9.2 <https://github.com/brsynth/neo4jsbml/tree/0.9.2>`__ (2023-02-23)
 ------------------------------------------------------------------------
 
 `Full
 Changelog <https://github.com/brsynth/neo4jsbml/compare/0.9.1...0.9.2>`__
 
-.. _section-6:
+.. _section-7:
 
 `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-7:
+.. _section-8:
 
 `0.9.0 <https://github.com/brsynth/neo4jsbml/tree/0.9.0>`__ (2023-01-27)
 ------------------------------------------------------------------------
@@ -107,15 +121,15 @@ Changelog <https://github.com/brsynth/neo4jsbml/compare/0.8.3...0.9.0>`__
    `#4 <https://github.com/brsynth/neo4jsbml/pull/4>`__
    (`dependabot[bot] <https://github.com/apps/dependabot>`__)
 
-.. _section-8:
+.. _section-9:
 
 `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-9:
+.. _section-10:
 
 `0.8.0 <https://github.com/brsynth/neo4jsbml/tree/0.8.0>`__ (2023-01-16)
 ------------------------------------------------------------------------

diff --git a/docs/applications.rst b/docs/applications.rst
@@ -10,7 +10,7 @@ Arrows modelisation
 ^^^^^^^^^^^^^^^^^^^
 :download:`(JSON schema) <_static/arrows/PathwayModelisation-2.0.2.json>`
 
-.. figure:: _static/arrows/PathwayModelisation-2.0.2.png
+.. figure:: _static/arrows/PathwayModelisation-2.0.2.svg
    :align: center
 
 Neo4jSbml
@@ -50,7 +50,7 @@ Arrows modelisation
 ^^^^^^^^^^^^^^^^^^^
 :download:`(JSON schema) <_static/arrows/PathwayModelisation-2.0.2.json>`
 
-.. figure:: _static/arrows/PathwayModelisation-2.0.2.png
+.. figure:: _static/arrows/PathwayModelisation-2.0.2.svg
     :align: center
 
 Neo4jSbml

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -130,20 +130,33 @@ To import your data with ``neo4jsbml`` into Neo4j, you will need:
 
 Plugins compatibility
 ~~~~~~~~~~~~~~~~~~~~~
++---------------------------------------------------------+---------------+
 | Package                                                 | Compatibility |
-| ------------------------------------------------------- | ------------- |
++=========================================================+===============+
 | Arrays                                                  | No            |
++---------------------------------------------------------+---------------+
 | Hierarchical Model Composition                          | No            |
++---------------------------------------------------------+---------------+
 | Distributions                                           | No            |
++---------------------------------------------------------+---------------+
 | Dynamic Structures                                      | No            |
++---------------------------------------------------------+---------------+
 | Flux Balance Constraints                                | Yes           |
++---------------------------------------------------------+---------------+
 | Groups                                                  | Yes           |
++---------------------------------------------------------+---------------+
 | Layout                                                  | Yes           |
++---------------------------------------------------------+---------------+
 | Extended MathML                                         | No            |
++---------------------------------------------------------+---------------+
 | Multistate, Multicomponent and Multicompartment Species | No            |
++---------------------------------------------------------+---------------+
 | Qualitative models                                      | Yes           |
++---------------------------------------------------------+---------------+
 | Rendering                                               | No            |
++---------------------------------------------------------+---------------+
 | Spatial Processes                                       | No            |
++---------------------------------------------------------+---------------+
 
 Export your data into Neo4j
 ---------------------------
@@ -167,24 +180,36 @@ To export your data with ``neo4jsbml`` into Neo4j, you will need:
 
 Plugins compatibility
 ~~~~~~~~~~~~~~~~~~~~~
++---------------------------------------------------------+---------------+
 | Package                                                 | Compatibility |
-| ------------------------------------------------------- | ------------- |
++=========================================================+===============+
 | Arrays                                                  | No            |
++---------------------------------------------------------+---------------+
 | Hierarchical Model Composition                          | No            |
++---------------------------------------------------------+---------------+
 | Distributions                                           | No            |
++---------------------------------------------------------+---------------+
 | Dynamic Structures                                      | No            |
++---------------------------------------------------------+---------------+
 | Flux Balance Constraints                                | No            |
++---------------------------------------------------------+---------------+
 | Groups                                                  | No            |
++---------------------------------------------------------+---------------+
 | Layout                                                  | No            |
++---------------------------------------------------------+---------------+
 | Extended MathML                                         | No            |
++---------------------------------------------------------+---------------+
 | Multistate, Multicomponent and Multicompartment Species | No            |
++---------------------------------------------------------+---------------+
 | Qualitative models                                      | No            |
++---------------------------------------------------------+---------------+
 | Rendering                                               | No            |
++---------------------------------------------------------+---------------+
 | Spatial Processes                                       | No            |
++---------------------------------------------------------+---------------+
 
-
-API
-~~~
+With python
+~~~~~~~~~~~
 .. code-block:: python
 
     from neo4jsbml import arrows, connect, sbml

diff --git a/src/neo4jsbml/_version.py b/src/neo4jsbml/_version.py
@@ -1,2 +1,2 @@
 __app_name__ = "neo4jsbml"
-__version__ = "0.12.0"
+__version__ = "1.0.0"