Merge branch 'master' into flb/review_checklist

EMMC-ASBL · Mar 24, 2022 · 2713190 · 2713190
2 parents 7f997d3 + 1ffc003
commit 2713190
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Showing 24 changed files with 263 additions and 150 deletions.
diff --git a/.github/workflows/cd_release.yml b/.github/workflows/cd_release.yml
@@ -19,12 +19,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 
@@ -47,9 +47,9 @@ jobs:
 
     - name: Update version and tag
       run: |
-        invoke setver --ver="${GITHUB_REF#refs/tags/}"
+        invoke setver --version="${GITHUB_REF#refs/tags/}"
 
-        git add oteapi/__init__.py CHANGELOG.md
+        git add oteapi_dlite/__init__.py CHANGELOG.md
         git commit -m "Release ${GITHUB_REF#refs/tags/} - Changelog"
 
         TAG_MSG=.github/utils/release_tag_msg.txt
@@ -101,13 +101,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
         ref: ${{ env.PUBLISH_UPDATE_BRANCH }}
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 

diff --git a/.github/workflows/ci_automerge_dependabot.yml b/.github/workflows/ci_automerge_dependabot.yml
@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
         ref: ${{ github.event.pull_request.head.ref }}

diff --git a/.github/workflows/ci_cd_updated_master.yml b/.github/workflows/ci_cd_updated_master.yml
@@ -18,7 +18,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ env.DEPENDABOT_BRANCH }}
         fetch-depth: 0
@@ -78,13 +78,13 @@ jobs:
 
     - name: Checkout repository
       if: env.RELEASE_RUN == 'false'
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 0
 
     - name: Set up Python 3.9
       if: env.RELEASE_RUN == 'false'
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 

diff --git a/.github/workflows/ci_dependabot.yml b/.github/workflows/ci_dependabot.yml
@@ -19,12 +19,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: master
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 
@@ -87,7 +87,7 @@ jobs:
 
     - name: Create PR
       id: cpr
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v4
       with:
         token: ${{ secrets.RELEASE_PAT }}
         commit-message: New @dependabot-fueled updates

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -14,10 +14,10 @@ jobs:
     # timeout-minutes: 2
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 
@@ -47,12 +47,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.9
 
@@ -85,12 +85,12 @@ jobs:
         python-version: ["3.9", "3.10"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version}}
 
@@ -120,12 +120,12 @@ jobs:
         python-version: ["3.9", "3.10"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version}}
 
@@ -151,9 +151,9 @@ jobs:
     # timeout-minutes: 5
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         with:
           python-version: 3.9
 
@@ -170,11 +170,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v3
       with:
         python-version: 3.9
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,19 +25,19 @@ repos:
       args: ["--profile", "black", "--filter-files", "--skip-gitignore"]
 
   - repo: https://github.com/ambv/black
-    rev: 21.12b0
+    rev: 22.1.0
     hooks:
     - id: black
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.2
+    rev: 1.7.4
     hooks:
     - id: bandit
       args: ["-r"]
       files: ^oteapi_dlite/.*$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.931
+    rev: v0.941
     hooks:
     - id: mypy
       exclude: ^tests/.*$

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,85 @@
 # Changelog
 
-This file will hold an auto-generated changelog for you project.
+## [Unreleased](https://github.com/EMMC-ASBL/oteapi-dlite/tree/HEAD)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.7...HEAD)
+
+**Fixed bugs:**
+
+- Tests are failing when using the `oteapi-core`@master [\#32](https://github.com/EMMC-ASBL/oteapi-dlite/issues/32)
+- Fix Excel parser [\#8](https://github.com/EMMC-ASBL/oteapi-dlite/issues/8)
+
+## [v0.0.7](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.7) (2022-03-17)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.6...v0.0.7)
+
+**Merged pull requests:**
+
+- Fix tests + excel parser [\#33](https://github.com/EMMC-ASBL/oteapi-dlite/pull/33) ([CasperWA](https://github.com/CasperWA))
+
+## [v0.0.6](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.6) (2022-03-16)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.5...v0.0.6)
+
+**Fixed bugs:**
+
+- Documentation issue [\#25](https://github.com/EMMC-ASBL/oteapi-dlite/issues/25)
+
+**Merged pull requests:**
+
+- Fix setup.cfg [\#31](https://github.com/EMMC-ASBL/oteapi-dlite/pull/31) ([jesper-friis](https://github.com/jesper-friis))
+- \[Auto-generated\] Update dependencies [\#30](https://github.com/EMMC-ASBL/oteapi-dlite/pull/30) ([TEAM4-0](https://github.com/TEAM4-0))
+- Corrected syntax in setup.cfg [\#28](https://github.com/EMMC-ASBL/oteapi-dlite/pull/28) ([jesper-friis](https://github.com/jesper-friis))
+
+## [v0.0.5](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.5) (2022-03-11)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.4...v0.0.5)
+
+**Merged pull requests:**
+
+- Updated strategy names [\#27](https://github.com/EMMC-ASBL/oteapi-dlite/pull/27) ([jesper-friis](https://github.com/jesper-friis))
+- \[Auto-generated\] Update dependencies [\#26](https://github.com/EMMC-ASBL/oteapi-dlite/pull/26) ([TEAM4-0](https://github.com/TEAM4-0))
+- Updated dlite image parse strategy according to changes in the image parse strategy in oteapi core PR \#108 [\#18](https://github.com/EMMC-ASBL/oteapi-dlite/pull/18) ([jesper-friis](https://github.com/jesper-friis))
+
+## [v0.0.4](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.4) (2022-03-07)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.3...v0.0.4)
+
+**Fixed bugs:**
+
+- Release workflow failing [\#22](https://github.com/EMMC-ASBL/oteapi-dlite/issues/22)
+
+**Merged pull requests:**
+
+- Fix folder reference in workflow [\#24](https://github.com/EMMC-ASBL/oteapi-dlite/pull/24) ([CasperWA](https://github.com/CasperWA))
+- Fix option name for `invoke setver` [\#23](https://github.com/EMMC-ASBL/oteapi-dlite/pull/23) ([CasperWA](https://github.com/CasperWA))
+
+## [v0.0.3](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.3) (2022-03-05)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/v0.0.2...v0.0.3)
+
+**Merged pull requests:**
+
+- Add serialise filter [\#17](https://github.com/EMMC-ASBL/oteapi-dlite/pull/17) ([jesper-friis](https://github.com/jesper-friis))
+- Added a simple filter that adds a collection to the session [\#15](https://github.com/EMMC-ASBL/oteapi-dlite/pull/15) ([jesper-friis](https://github.com/jesper-friis))
+
+## [v0.0.2](https://github.com/EMMC-ASBL/oteapi-dlite/tree/v0.0.2) (2022-03-05)
+
+[Full Changelog](https://github.com/EMMC-ASBL/oteapi-dlite/compare/04843680b62d6bb3bc16e5ff644edbcc40892f31...v0.0.2)
+
+**Closed issues:**
+
+- Add CI/CD workflow\(s\) [\#3](https://github.com/EMMC-ASBL/oteapi-dlite/issues/3)
+
+**Merged pull requests:**
+
+- Relaxed dependencies [\#16](https://github.com/EMMC-ASBL/oteapi-dlite/pull/16) ([jesper-friis](https://github.com/jesper-friis))
+- fix ci cd workflow [\#14](https://github.com/EMMC-ASBL/oteapi-dlite/pull/14) ([jesper-friis](https://github.com/jesper-friis))
+- Add MANIFEST.in [\#9](https://github.com/EMMC-ASBL/oteapi-dlite/pull/9) ([CasperWA](https://github.com/CasperWA))
+- Image parser [\#7](https://github.com/EMMC-ASBL/oteapi-dlite/pull/7) ([TorgeirUstad](https://github.com/TorgeirUstad))
+- Add CI/CD  [\#4](https://github.com/EMMC-ASBL/oteapi-dlite/pull/4) ([jesper-friis](https://github.com/jesper-friis))
+- Parse excel [\#1](https://github.com/EMMC-ASBL/oteapi-dlite/pull/1) ([jesper-friis](https://github.com/jesper-friis))
+
+
+
+\* *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
@@ -31,4 +31,8 @@ OTEAPI DLite Plugin has been created via the [cookiecutter](https://cookiecutter
 
 OTEAPI DLite Plugin has been supported by the following projects:
 
-- **OntoTrans** (2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 862136.
+* __OntoTrans__ (2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 862136.
+
+* __VIPCOAT__ (2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 952903.
+
+* __OpenModel__ (2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 953167.
diff --git a/docs/index.md b/docs/index.md
@@ -31,4 +31,8 @@ OTEAPI DLite Plugin has been created via the [cookiecutter](https://cookiecutter
 
 OTEAPI DLite Plugin has been supported by the following projects:
 
-- **OntoTrans** (2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement n. 862136.
+* __OntoTrans__ (2020-2024) that receives funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 862136.
+
+* __VIPCOAT__ (2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 952903.
+
+* __OpenModel__ (2021-2025) receives funding from the European Union’s Horizon 2020 Research and Innovation Programme - DT-NMBP-11-2020 Open Innovation Platform for Materials Modelling, under Grant Agreement no: 953167.
diff --git a/oteapi_dlite/__init__.py b/oteapi_dlite/__init__.py
@@ -6,6 +6,6 @@
 Created from cookiecutter-oteapi-plugin, SINTEF, 2022
 """
 
-__version__ = "0.0.3"
+__version__ = "0.0.7"
 __author__ = "team4.0@sintef.no"
 __author_email__ = "team4.0@sintef.no"
diff --git a/oteapi_dlite/strategies/filter.py b/oteapi_dlite/strategies/filter.py
@@ -1,16 +1,16 @@
 """Trivial filter that adds an empty collection to the session."""
 # pylint: disable=no-self-use,unused-argument
-from dataclasses import dataclass
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Dict
 
 import dlite
+from oteapi.models import FilterConfig
+from pydantic import Field
+from pydantic.dataclasses import dataclass
 
 from oteapi_dlite.models import DLiteSessionUpdate
 
 if TYPE_CHECKING:
-    from typing import Any, Dict, Optional
-
-    from oteapi.models import FilterConfig
+    from typing import Optional
 
 
 @dataclass
@@ -19,11 +19,18 @@ class CreateCollectionStrategy:
 
     **Registers strategies**:
 
-    - `("filterType", "create_collection")`
+    - `("filterType", "dlite/create-collection")`
 
     """
 
-    filter_config: "FilterConfig"
+    filter_config: FilterConfig
+
+    # Find a better way to keep collections alive!!!
+    # Need to be `Any`, because otherwise `pydantic` complains.
+    collection_refs: Dict[str, Any] = Field(
+        {},
+        description="A dictionary of DLite Collections.",
+    )
 
     def initialize(
         self, session: "Optional[Dict[str, Any]]" = None
@@ -37,7 +44,7 @@ def initialize(
 
         # Save reference to the collection to ensure that it lives as long as
         # the session does
-        session["_collection_ref"] = coll
+        self.collection_refs[coll.uuid] = coll
 
         return DLiteSessionUpdate(collection_id=coll.uuid)