diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index c166302..5d8391f 100644 --- 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 index a336d0d..1b6a882 100644 --- 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 index 5328972..f3c8ece 100644 --- 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 index 0ee7adb..e3d39ba 100644 --- a/docs/CHANGELOG.data.rst +++ b/docs/CHANGELOG.data.rst @@ -1,6 +1,20 @@ Changelog ========= +`0.12.0 `__ (2023-10-08) +-------------------------------------------------------------------------- + +`Full +Changelog `__ + +**Merged pull requests:** + +- Take into account ``annotation`` field + `#15 `__ + (`guillaume-gricourt `__) + +.. _section-1: + `0.11.2 `__ (2023-10-07) -------------------------------------------------------------------------- @@ -19,7 +33,7 @@ Changelog `__ `#11 `__ (`guillaume-gricourt `__) -.. _section-1: +.. _section-2: `0.11.1 `__ (2023-09-22) -------------------------------------------------------------------------- @@ -39,7 +53,7 @@ Changelog `__ `#8 `__ (`dependabot[bot] `__) -.. _section-2: +.. _section-3: `0.11.0 `__ (2023-03-28) -------------------------------------------------------------------------- @@ -53,7 +67,7 @@ Changelog `__ `#7 `__ (`guillaume-gricourt `__) -.. _section-3: +.. _section-4: `0.10.1 `__ (2023-03-17) -------------------------------------------------------------------------- @@ -61,7 +75,7 @@ Changelog `__ `Full Changelog `__ -.. _section-4: +.. _section-5: `0.10.0 `__ (2023-03-17) -------------------------------------------------------------------------- @@ -77,7 +91,7 @@ Changelog `__ - Read the docs `#5 `__ (`guillaume-gricourt `__) -.. _section-5: +.. _section-6: `0.9.2 `__ (2023-02-23) ------------------------------------------------------------------------ @@ -85,7 +99,7 @@ Changelog `__ `Full Changelog `__ -.. _section-6: +.. _section-7: `0.9.1 `__ (2023-02-21) ------------------------------------------------------------------------ @@ -93,7 +107,7 @@ Changelog `__ `Full Changelog `__ -.. _section-7: +.. _section-8: `0.9.0 `__ (2023-01-27) ------------------------------------------------------------------------ @@ -107,7 +121,7 @@ Changelog `__ `#4 `__ (`dependabot[bot] `__) -.. _section-8: +.. _section-9: `0.8.3 `__ (2023-01-16) ------------------------------------------------------------------------ @@ -115,7 +129,7 @@ Changelog `__ `Full Changelog `__ -.. _section-9: +.. _section-10: `0.8.0 `__ (2023-01-16) ------------------------------------------------------------------------ diff --git a/docs/applications.rst b/docs/applications.rst index 26a78c2..6a9306c 100644 --- 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 index 15bf3a8..e6979c5 100644 --- 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 index 3ab2edf..f4b4068 100644 --- 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"