Merge pull request #7 from dilpath/ci_linter

Add linter to ci, rename files for easier discovery

Author: BSnelling

.github/workflows/ci.yml

@@ -0,0 +1,27 @@
+name: quality
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest pyyaml
+          # TODO switch to pypi
+          python -m pip install "petab_sciml @ git+https://github.com/PEtab-dev/petab_sciml.git"
+          python -m pip install "petab @ git+https://github.com/PEtab-dev/libpetab-python.git"
+
+      - name: Lint problems
+        run: pytest tests/test_lint_problems.py -v

.gitignore

@@ -0,0 +1,3 @@
+__pycache__/
+*.py[cod]
+.pytest_cache/

…/hybridization_Dandekar_Patterns2020.tsv …Dandekar_Patterns2020/hybridizations.tsvBenchmark-Models/Dandekar_Patterns2020/hybridization_Dandekar_Patterns2020.tsv renamed to Benchmark-Models/Dandekar_Patterns2020/hybridizations.tsv Benchmark-Models/Dandekar_Patterns2020/hybridization_Dandekar_Patterns2020.tsv renamed to Benchmark-Models/Dandekar_Patterns2020/hybridizations.tsv

@@ -1,26 +1,26 @@
 format_version: 2.0.0
-parameter_files:
-  - parameters_Ko_NeurIPS2023.tsv
 model_files:
   model:
-    location: model_Ko_NeurIPS2023.xml
+    location: ../model.xml
     language: sbml
+parameter_files:
+  - ../parameters.tsv
 measurement_files:
-  - measurements_train_Ko_NeurIPS2023.tsv
+  - measurements_validation.tsv
 observable_files:
-  - observables_Ko_NeurIPS2023.tsv
+  - ../observables.tsv
 mapping_files:
-  - mapping_Ko_NeurIPS2023.tsv
+  - ../mappings.tsv
 extensions:
   sciml:
     version: 0.1.0
     required: true
     neural_networks:
       net1:
-        location: net1_Ko_NeurIPS2023.yaml
+        location: ../nn_model_net1.yaml
         format: yaml
         pre_initialization: false
     hybridization_files:
-      - hybridization_Ko_NeurIPS2023.tsv
+      - ../hybridizations.tsv
     array_files:
-      - ps_net1_Ko_NeurIPS2023.hdf5
+      - ../parameters_net1.hdf5