Clean up (#195)

1. Remove old CLI "apps" that aren't used anymore 2. Remove pydantic 1 testing 3. Add contribution guide for sources 4. Don't output date if there's a data version available 5. Remove redundant testing from bioregistry
biopragmatics · Oct 22, 2024 · e3e7139 · e3e7139
1 parent 9a2c749
commit e3e7139
Show file tree

Hide file tree

Showing 27 changed files with 71 additions and 699 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.12" ]
+        python-version: [ "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -46,7 +46,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get install graphviz
-          pip install tox
+          pip install tox tox-uv
       - name: Check RST conformity with doc8
         run: tox -e doc8
       - name: Check README.rst
@@ -60,7 +60,6 @@ jobs:
       matrix:
         os: [ ubuntu-latest ]
         python-version: [ "3.9", "3.12" ]
-        pydantic: [ "pydantic1", "pydantic2" ]
         exclude:
           - os: windows-latest
             python-version: 3.9
@@ -73,7 +72,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get install graphviz
-          pip install tox
+          pip install tox tox-uv
       - name: Test with pytest
         run:
-          tox -e py-${{ matrix.pydantic }}
+          tox -e py
diff --git a/benchmarking/resolver_benchmark.py b/benchmarking/resolver_benchmark.py
diff --git a/setup.cfg b/setup.cfg
@@ -59,12 +59,13 @@ install_requires =
     tabulate
     cachier
     pystow>=0.2.7
-    bioversions>=0.5.202
+    bioversions>=0.5.514
     bioregistry>=0.10.20
     bioontologies>=0.4.0
     zenodo-client>=0.0.5
     class_resolver
     psycopg2-binary
+    pydantic>=2.0
     # Resource Downloaders
     drugbank_downloader
     chembl_downloader

diff --git a/src/pyobo/apps/__init__.py b/src/pyobo/apps/__init__.py
diff --git a/src/pyobo/apps/cli.py b/src/pyobo/apps/cli.py
diff --git a/src/pyobo/apps/gilda/__init__.py b/src/pyobo/apps/gilda/__init__.py
diff --git a/src/pyobo/apps/gilda/__main__.py b/src/pyobo/apps/gilda/__main__.py
diff --git a/src/pyobo/apps/gilda/app.py b/src/pyobo/apps/gilda/app.py
diff --git a/src/pyobo/apps/gilda/cli.py b/src/pyobo/apps/gilda/cli.py
diff --git a/src/pyobo/apps/gilda/templates/base.html b/src/pyobo/apps/gilda/templates/base.html
diff --git a/src/pyobo/apps/gilda/templates/home.html b/src/pyobo/apps/gilda/templates/home.html
diff --git a/src/pyobo/apps/gilda/templates/matches.html b/src/pyobo/apps/gilda/templates/matches.html
diff --git a/src/pyobo/apps/mapper/__init__.py b/src/pyobo/apps/mapper/__init__.py
diff --git a/src/pyobo/apps/mapper/__main__.py b/src/pyobo/apps/mapper/__main__.py
diff --git a/src/pyobo/apps/mapper/cli.py b/src/pyobo/apps/mapper/cli.py