Merge pull request #22 from biosimulators/fix-local-parameters

Handle local parameters (again).

.github/actions/setup-poetry-env/action.yml

@@ -0,0 +1,42 @@
+name: "setup-poetry-env"
+description: "Composite action to setup the Python and poetry environment."
+
+inputs:
+  python-version:
+    required: false
+    description: "The python version to use"
+    default: "3.11"
+
+runs:
+  using: "composite"
+  steps:
+    - name: Set up python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install Poetry
+      env:
+        POETRY_VERSION: "1.7.1"
+      run: curl -sSL https://install.python-poetry.org | python - -y
+      shell: bash
+
+    - name: Add Poetry to Path
+      run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      shell: bash
+
+#    - name: Configure Poetry virtual environment in project
+#      run: poetry config virtualenvs.in-project true
+#      shell: bash
+
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v4
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }}
+
+    - name: Install dependencies
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction
+      shell: bash

.github/workflows/ci.yml

@@ -70,36 +70,11 @@ jobs:
       #############################################
       ## Install package and its dependencies
       #############################################
-      - name: Install Python
-        uses: actions/setup-python@v3
-        with:
-          python-version: '3.11'
-
-      - name: Setup pip cache
-        uses: actions/cache@v3
-        with:
-          path: /opt/hostedtoolcache/Python
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install libXML2
-        run: |
-          sudo apt-get update -y
-          sudo apt-get install -y --no-install-recommends libxml2
-
-      - name: Install pip
-        run: |
-          python -m pip install pip==23.0.0
-          python -m pip install pip==23.0.0
-          python -m pip --version
-          #python -m pip install --upgrade setuptools
-          #python -m setuptools --version
-
-
-      - name: Install package
-        run: |
-          python -m pip install .[all]
+      # install package
+      -   name: Set up the environment
+          uses: ./.github/actions/setup-poetry-env
+          with:
+              python-version: "3.11"
 
       #############################################
       ## Lint
@@ -125,6 +100,7 @@ jobs:
           fi
 
           echo "version=$version" >> $GITHUB_OUTPUT
+          echo "version=$version"
 
       - id: get-docker-image-tag
         name: Determine Docker image tag
@@ -172,7 +148,7 @@ jobs:
         run: python -m pytest tests/ --cov=biosimulators_tellurium --cov-report=xml
 
       - name: Upload the coverage report to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests

Dockerfile

@@ -12,7 +12,7 @@
 #       -o /root/out
 
 # Base OS
-FROM python:3.9-slim-buster
+FROM python:3.11-slim-buster
 
 ARG VERSION="0.1.25"
 ARG SIMULATOR_VERSION="2.2.10"
@@ -29,7 +29,7 @@ LABEL \
     org.opencontainers.image.vendor="BioSimulators Team" \
     org.opencontainers.image.licenses="Apache-2.0" \
     \
-    base_image="python:3.9-slim-buster" \
+    base_image="python:3.11-slim-buster" \
     version="${VERSION}" \
     software="tellurium" \
     software.version="${SIMULATOR_VERSION}" \

biosimulators_tellurium/_version.py

@@ -1 +1 @@
-__version__ = '0.1.43'
+__version__ = '0.1.44'

biosimulators_tellurium/core.py

@@ -431,7 +431,8 @@ def preprocess_sed_task(task, variables, config=None, simulator_config=None):
                                   warning_summary='Model `{}` may be invalid.'.format(model.id))
 
         # read model
-        road_runner = roadrunner.RoadRunner(model.source)
+        road_runner = roadrunner.RoadRunner()
+        road_runner = roadrunner.RoadRunner(road_runner.getParamPromotedSBML(model.source))
 
         # get algorithm to execute
         algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
@@ -583,7 +584,7 @@ def get_model_change_target_tellurium_change_map(model_etree, changes, alg_kisao
     Returns:
         :obj:`dict`: dictionary that maps the targets of changes to their corresponding tellurium identifiers
     """
-    change_targets_to_sbml_ids = validation.validate_target_xpaths(changes, model_etree, attr='id')
+    change_targets_to_sbml_ids = validation.validate_target_xpaths(changes, model_etree, attr='id', separator="_")
 
     species_ids = model.getFloatingSpeciesIds() + model.getBoundarySpeciesIds()
     component_ids = species_ids + model.getGlobalParameterIds() + model.getCompartmentIds()