Refactor PyCIEMSS to use ChiRho and remove stale functionality (#396)

* remove all files except interfaces and integration demo * remove tests * minor refactor of dependencies and added lint * added back in github workflows * add quote around 3.10 * added makefile for offline lint testing * ran make format * removed Ensemble * added types for interfaces, and deleted ODE implementations * lint * fixed makefile for tests * get test_modules_import working * lint * remove src from directory * remove stale notebooks * remove src from lint scripts * modify setup.cfg * added pytest cov * remove .gitignore in notebook * remove stale INSTALL.md * remove pytest-cov * rename test to tests * update scripts with new tests filepath * fix Makefile to point to correct tests * AMR and MIRA integration with Chirho (#398) * added scaffolding for ODE * tidying and linting * get modules importing and update mira * got initial state working * revise tests and lint * manually added torchdiffeq to requirements * revert debugging * remove empty interfaces * minor refactor * minor refactor * moved compile_deriv and compile_initial_state into init method for other factory methods to have access to. also removed eval_rate_law, because that might be confusing if users change it and it does nothing * typo * `simulate` TA4 interface (#399) * progress towards TA4 interfaces * minor tidying, still incomplete * more tidying * remove attempt at pickling, and added intervention test * dynamic intervention tests working * got predictive working * added additional test * update types * update types * fix upstream time collisions in ChiRho (#400) * rename simulate to sample * add pyciemss_logging_wrapper and documentation * revise tests * remove placeholder parameters (#403) * Support for regulatory networks (#404) * add support for regnet now that mira has been fixed * lint * uncomment other mistakenly commented tests * swap out dict access for explicit iteration * lint * Remove package finding AND add to module exports (#407) * Remove package finding AND add to module exports * Clear out top-level `__init__.py` * Reinclude explicit exports * Include subpackages * Skip incorrect lint error * reorder imports for lint * revert previous commit and add missing space before noqa --------- Co-authored-by: Sam Witty <[email protected]> * Add basic output formatting (#405) * initial pass at output processing * lint * add pandas and numpy dependencies * remove outdated docstring * Remove package finding AND add to module exports (#407) (#409) * Remove package finding AND add to module exports * Clear out top-level `__init__.py` * Reinclude explicit exports * Include subpackages * Skip incorrect lint error * reorder imports for lint * revert previous commit and add missing space before noqa --------- Co-authored-by: Five Grant <[email protected]> --------- Co-authored-by: Five Grant <[email protected]> * `calibrate` TA4 interface (#401) * progress towards TA4 interfaces * minor tidying, still incomplete * more tidying * remove attempt at pickling, and added intervention test * dynamic intervention tests working * got predictive working * added additional test * update types * update types * fix upstream time collisions in ChiRho (#400) * early progress on calibration * added noise model * minor change to sampling interface * more progress * lint * lint * more merge fixes * add back petri models * temporary test fixtures while waiting on PRs to land * make * update tests and lint * lint * got calibrate working * move start_time to kwarg * added test of simulating from deterministic parameters * lint * add documentation * update fixtures to include permalink to models * remove aggregate parameters * Basic functionality for sampling from an ensemble of dynamical systems models (#411) * first pass at ensemble * revision to tests * added ensemble sampling interface and tests * lint nit * register nit * added documentation? * line length * lint * Update test fixtures to include new gold-standard AMRs (#415) * scaled noise according to size of state variable * update AMRs * add back regnet and stockflow * trivial change to trigger CI build * Add basic integration notebook and CI for testing notebooks (#416) * add basic notebook and nbval test * nbval CI * make ensemble a module * changed imports in CI builds and added imports throughout * reran interfaces * lint * Add observables to sample output (#412) * first pass at observables * lint * fix result processing * add correction with empty observables * minor fix to name * nitpick on name * retrigger checks * updating urls for petri and stock flow example amrs (#419) * updating urls for petri and stock flow example amrs * Shortening url lengths to address linting issue * Fixing urls for linting issue * Changing AMR url in interfaces notebook * Updating model_2_path to correct url * Bump ChiRho version in dependencies and update any changes resulting from API changes (#422) * bumped chirho version * pull out solver * removed IEL and pulled out solver * revised tests * reverted fixtures chagne * lint * nit * updated compiled dynamics * updated tests * lint * nit * revert changes to fixtures * updating urls for petri and stock flow example amrs (#419) (#423) * updating urls for petri and stock flow example amrs * Shortening url lengths to address linting issue * Fixing urls for linting issue * Changing AMR url in interfaces notebook * Updating model_2_path to correct url Co-authored-by: sabinala <[email protected]> * reverted changes to types * lint --------- Co-authored-by: sabinala <[email protected]> * scale back tests (#427) * Parameter Intervention (#424) * added separate persistent params to make bookkeeping interventions more reliable * implemented parameter intervention * added tests with annotation of important paramaters * lint * added dynamic interventions on parameters (#425) * lint and doc * Add interfaces and refactor tests (#426) * added interfaces and refactored interruptions * refactor and add to tests * scale back tests (#427) * easier tests * Adding regnet urls to fixtures, and limiting number of examples to three per type (#428) * Update fixtures.py to include regnets and three examples per type * Update fixtures.py * lint --------- Co-authored-by: Sam Witty <[email protected]> * Add parameter interventions to calibrate and refactor interface tests (#429) * Added parameter interventions to calibrate * refactored calibrate tests * refactor observables * fix bug in test * ignore test with underflow * made interventions a bit lighter * Add datafile input for `calibrate` (#432) * add data loading utilities * added data loading utilities to calibrate interface * updated tests with new data loading utilities * lint * bump pyciemss version (#433) * bump pyciemss version * remove stale setup config --------- Co-authored-by: Five Grant <[email protected]> Co-authored-by: sabinala <[email protected]>
ciemss · Dec 18, 2023 · 4ca1d6a · 4ca1d6a
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diff --git a/.github/workflows/main.yml → .github/workflows/integration-workbench.yml b/.github/workflows/main.yml → .github/workflows/integration-workbench.yml
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -0,0 +1,38 @@
+name: Lint
+
+on:
+  push:
+    branches: [ main, staging-refactor ]
+  pull_request:
+    branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: pip cache
+        uses: actions/cache@v1
+        with:
+          path: ~/.cache/pip
+          key: lint-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            lint-pip-
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Lint
+        run: ./scripts/lint.sh
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,53 @@
+name: Test
+
+on:
+  push:
+    branches: [ main, staging-refactor ]
+  pull_request:
+    branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8, 3.9, '3.10']
+        os: [ubuntu-latest]  # , macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Ubuntu cache
+        uses: actions/cache@v1
+        if: startsWith(matrix.os, 'ubuntu')
+        with:
+          path: ~/.cache/pip
+          key:
+            ${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: macOS cache
+        uses: actions/cache@v1
+        if: startsWith(matrix.os, 'macOS')
+        with:
+          path: ~/Library/Caches/pip
+          key:
+            ${{ matrix.os }}-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ matrix.os }}-${{ matrix.python-version }}-
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Test
+        shell: bash
+        run: |
+          pytest tests/ -s -n auto
diff --git a/.github/workflows/test_notebooks.yml b/.github/workflows/test_notebooks.yml
@@ -0,0 +1,40 @@
+name: Test notebooks
+
+on:
+    schedule:
+      - cron: '0 0 * * 6'  # Run at midnight on Saturdays
+    push:
+      branches: [ main, staging-refactor ]
+    pull_request: 
+      branches: [ main, staging-refactor ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+        - uses: actions/checkout@v2
+
+        - name: pip cache
+          uses: actions/cache@v1
+          with:
+            path: ~/.cache/pip
+            key: lint-pip-${{ hashFiles('**/pyproject.toml') }}
+            restore-keys: |
+              lint-pip-
+
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v1
+          with:
+            python-version: ${{ matrix.python-version }}
+
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install -e .[tests]
+    
+        - name: Run Notebook Test
+          run: python -m pytest --nbval-lax docs/source/interfaces.ipynb
diff --git a/.gitignore b/.gitignore
@@ -339,3 +339,4 @@ venv/
 *~
 *_schema.json
 *data_with_missing_entries.csv
+*.nix
diff --git a/INSTALL.md b/INSTALL.md
diff --git a/Makefile b/Makefile
@@ -0,0 +1,10 @@
+lint: FORCE
+	./scripts/lint.sh
+
+format:
+	./scripts/clean.sh
+
+tests: lint FORCE
+	pytest -v tests -n auto
+
+FORCE:
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -19,7 +19,7 @@
 exclude_patterns = []
 
 extensions += ['sphinx.ext.autodoc', 'autoapi.extension']
-autoapi_dirs = ['../../src']
+autoapi_dirs = ['../../pyciemss']
 
 
 # -- Options for HTML output -------------------------------------------------