add notebook examples, configure precommit correctly

Author: esoteric-ephemera

.DS_Store

@@ -33,7 +33,7 @@ jobs:
           cache: "pip"
       - name: Install dependencies
         run: |
-          python${{ matrix.python-version }} -m pip install --upgrade "pip<25.3" build pip-tools
+          python${{ matrix.python-version }} -m pip install --upgrade "pip<25.3" build pip-tools pre-commit
           python${{ matrix.python-version }} -m piptools compile --extra dev -o requirements.txt mpcontribs-client/setup.py mpcontribs-api/setup.py
           python${{ matrix.python-version }} -m pip install -r requirements.txt
           cd mpcontribs-api && python${{ matrix.python-version }} -m pip install --no-deps .
@@ -47,6 +47,13 @@ jobs:
         run: |
           $env:SSL_CERT_FILE=$(python${{ matrix.python-version }} -m certifi)
           echo "SSL_CERT_FILE=$env:SSL_CERT_FILE" >> $GITHUB_ENV
+
+      - name: Run pre-commit
+        run: |
+          python${{ matrix.python-version }} -m pip install pre-commit
+          pre-commit install
+          pre-commit run --all-files
+
       - name: Test Client and build
         env:
           MPCONTRIBS_API_KEY: ${{ secrets.MPCONTRIBS_API_KEY }}
@@ -58,22 +65,11 @@ jobs:
           python${{ matrix.python-version }} -m pycodestyle --max-line-length 100 .
           python${{ matrix.python-version }} -m pytest -v -s --cov=mpcontribs/client --cov-report=term-missing --cov-report=xml --ignore=bravado
           python${{ matrix.python-version }} -m build --outdir ../dist
-          cd ..
-
-      - name: Install dependencies for lux
-        run: |
-          python${{ matrix.python-version }} -m pip install --upgrade pip
-          pip install -r mpcontribs-lux/requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
-
-      - name: Run pre-commit for lux
-        run: |
-          python${{ matrix.python-version }} -m pip install pre-commit
-          pre-commit install
-          pre-commit run --files mpcontribs-lux/mpcontribs/lux/*
 
-      - name: Test lux with pytest
+      - name: Install lux and test with pytest
         run: |
           cd mpcontribs-lux
+          python${{ matrix.python-version }} -m pip install -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
           python${{ matrix.python-version }} -m pip install -e .
           python${{ matrix.python-version }} -m pytest -n auto -x --cov=mpcontribs/lux --cov-report=xml
 

.github/workflows/testing.yml

@@ -2,8 +2,12 @@ exclude: |
   (?x)(
       ^mpcontribs-portal/mpcontribs/users/|
       ^binder/|
+      ^mpcontribs-api/|
       ^mpcontribs-ingester/|
-      ^mpcontribs-api/mpcontribs/api/redox_thermo_csp/
+      ^mpcontribs-io/|
+      ^mpcontribs-kernel-gateway/|
+      ^mpcontribs-portal/|
+      ^mpcontribs-serverless/
   )
 
 repos:
@@ -34,7 +38,7 @@ repos:
     rev: 25.9.0
     hooks:
       - id: black
-      
+
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.1
     hooks:

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ Set the environment variable `SSL_CERT_FILE` to `$(python -m certifi)`.
 OverflowError: timeout value is too large
 ```
 
-Install the bravado fork ([PR](https://github.com/Yelp/bravado/pull/472)) manually via  
+Install the bravado fork ([PR](https://github.com/Yelp/bravado/pull/472)) manually via
 ```
 pip install "bravado[fido] @ git+https://github.com/tschaume/bravado@9ce06f2df7118e16af4a3d3fdc21ccfeedc5cd50#egg=bravado-11.0.3"
 ```

mpcontribs-client/README.md

@@ -71,12 +71,12 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
-jsonschema[format-nongpl]==4.25.1
     # via
     #   bravado-core
     #   swagger-spec-validator
 jsonschema-specifications==2025.9.1
+    # via bravado-core
+jsonschema[format-nongpl]==4.25.1
     # via jsonschema
 kiwisolver==1.4.9
     # via matplotlib

mpcontribs-client/requirements/deployment.txt

@@ -71,12 +71,12 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
-jsonschema[format-nongpl]==4.25.1
     # via
     #   bravado-core
     #   swagger-spec-validator
 jsonschema-specifications==2025.9.1
+    # via bravado-core
+jsonschema[format-nongpl]==4.25.1
     # via jsonschema
 kiwisolver==1.4.9
     # via matplotlib

mpcontribs-client/requirements/ubuntu-latest_py3.11.txt

@@ -79,12 +79,12 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
-jsonschema[format-nongpl]==4.25.1
     # via
     #   bravado-core
     #   swagger-spec-validator
 jsonschema-specifications==2025.9.1
+    # via bravado-core
+jsonschema[format-nongpl]==4.25.1
     # via jsonschema
 kiwisolver==1.4.9
     # via matplotlib

mpcontribs-client/requirements/ubuntu-latest_py3.11_extras.txt

@@ -71,12 +71,12 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
-jsonschema[format-nongpl]==4.25.1
     # via
     #   bravado-core
     #   swagger-spec-validator
 jsonschema-specifications==2025.9.1
+    # via bravado-core
+jsonschema[format-nongpl]==4.25.1
     # via jsonschema
 kiwisolver==1.4.9
     # via matplotlib

mpcontribs-client/requirements/ubuntu-latest_py3.12.txt

@@ -79,12 +79,12 @@ json2html==1.3.0
 jsonpointer==3.0.0
     # via jsonschema
 jsonref==1.1.0
-    # via bravado-core
-jsonschema[format-nongpl]==4.25.1
     # via
     #   bravado-core
     #   swagger-spec-validator
 jsonschema-specifications==2025.9.1
+    # via bravado-core
+jsonschema[format-nongpl]==4.25.1
     # via jsonschema
 kiwisolver==1.4.9
     # via matplotlib

mpcontribs-client/requirements/ubuntu-latest_py3.12_extras.txt

@@ -6,7 +6,7 @@
 except ImportError:
     create_app = None
 
-os.environ['MPCONTRIBS_DB_NAME'] = 'mpcontribs-test'
+os.environ["MPCONTRIBS_DB_NAME"] = "mpcontribs-test"
 
 
 @pytest.fixture()