op-engine 0.1.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (44) hide show
  1. op_engine-0.1.0/.github/workflows/ci.yaml +95 -0
  2. op_engine-0.1.0/.github/workflows/gh-pages.yaml +108 -0
  3. op_engine-0.1.0/.github/workflows/release.yaml +194 -0
  4. op_engine-0.1.0/.gitignore +187 -0
  5. op_engine-0.1.0/LICENSE +19 -0
  6. op_engine-0.1.0/PKG-INFO +142 -0
  7. op_engine-0.1.0/README.md +98 -0
  8. op_engine-0.1.0/docs/api-reference/.gitignore +1 -0
  9. op_engine-0.1.0/docs/development/creating-a-release.md +129 -0
  10. op_engine-0.1.0/docs/guides/getting-started.md +16 -0
  11. op_engine-0.1.0/docs/index.md +3 -0
  12. op_engine-0.1.0/examples/__init__.py +2 -0
  13. op_engine-0.1.0/examples/biogeochemical_network.py +1304 -0
  14. op_engine-0.1.0/examples/simple_sir.py +235 -0
  15. op_engine-0.1.0/flepimop2-op_engine/LICENSE +676 -0
  16. op_engine-0.1.0/flepimop2-op_engine/README.md +3 -0
  17. op_engine-0.1.0/flepimop2-op_engine/pyproject.toml +85 -0
  18. op_engine-0.1.0/flepimop2-op_engine/src/flepimop2/engine/op_engine/__init__.py +246 -0
  19. op_engine-0.1.0/flepimop2-op_engine/src/flepimop2/engine/op_engine/config.py +148 -0
  20. op_engine-0.1.0/flepimop2-op_engine/src/flepimop2/engine/op_engine/py.typed +0 -0
  21. op_engine-0.1.0/flepimop2-op_engine/tests/conftest.py +19 -0
  22. op_engine-0.1.0/flepimop2-op_engine/tests/data/config.yaml +34 -0
  23. op_engine-0.1.0/flepimop2-op_engine/tests/data/sir.py +34 -0
  24. op_engine-0.1.0/flepimop2-op_engine/tests/test_config.py +179 -0
  25. op_engine-0.1.0/flepimop2-op_engine/tests/test_engine.py +355 -0
  26. op_engine-0.1.0/flepimop2-op_engine/tests/test_integration_cli.py +56 -0
  27. op_engine-0.1.0/justfile +166 -0
  28. op_engine-0.1.0/mkdocs.yml +53 -0
  29. op_engine-0.1.0/overrides/main.html +8 -0
  30. op_engine-0.1.0/pyproject.toml +97 -0
  31. op_engine-0.1.0/scripts/__init__.py +1 -0
  32. op_engine-0.1.0/scripts/api-reference.py +199 -0
  33. op_engine-0.1.0/scripts/release_validate.py +94 -0
  34. op_engine-0.1.0/src/op_engine/__init__.py +53 -0
  35. op_engine-0.1.0/src/op_engine/core_solver.py +2093 -0
  36. op_engine-0.1.0/src/op_engine/matrix_ops.py +1166 -0
  37. op_engine-0.1.0/src/op_engine/model_core.py +511 -0
  38. op_engine-0.1.0/src/op_engine/py.typed +0 -0
  39. op_engine-0.1.0/tests/conftest.py +3 -0
  40. op_engine-0.1.0/tests/op_engine/test__version__.py +8 -0
  41. op_engine-0.1.0/tests/op_engine/test_core_solver_accuracy.py +733 -0
  42. op_engine-0.1.0/tests/op_engine/test_core_solver_plumbing.py +361 -0
  43. op_engine-0.1.0/tests/op_engine/test_matrix_ops.py +660 -0
  44. op_engine-0.1.0/tests/op_engine/test_model_core.py +437 -0
@@ -0,0 +1,95 @@
1
+ ---
2
+ name: 'CI'
3
+
4
+ 'on':
5
+ pull_request:
6
+ branches:
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+ - 'main'
8
+ workflow_dispatch:
9
+
10
+ concurrency:
11
+ group: ${{ github.workflow }}-${{ github.ref }}
12
+ cancel-in-progress: true
13
+
14
+ permissions:
15
+ contents: 'read'
16
+
17
+ jobs:
18
+ build-check:
19
+ name: 'Build Check (${{ matrix.python-version }})'
20
+ runs-on: 'ubuntu-latest'
21
+ strategy:
22
+ matrix:
23
+ python-version:
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+ - '3.12'
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+ steps:
26
+ - name: 'Install just'
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+ uses: 'extractions/setup-just@v3'
28
+ - name: 'Checkout repository'
29
+ uses: 'actions/checkout@v6'
30
+ with:
31
+ persist-credentials: false
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+ - name: 'Setup uv with python ${{ matrix.python-version }}'
33
+ uses: 'astral-sh/setup-uv@v7.2.0'
34
+ with:
35
+ enable-cache: true
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+ cache-dependency-glob: 'pyproject.toml'
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+ python-version: '${{ matrix.python-version }}'
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+ - name: 'Run Build Check'
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+ run: 'just build-check'
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+ env:
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+ UV_PYTHON_VERSION: '${{ matrix.python-version }}'
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+ ci:
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+ name: 'CI (${{ matrix.python-version }})'
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+ needs:
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+ - 'docs'
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+ - 'build-check'
47
+ runs-on: 'ubuntu-latest'
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+ strategy:
49
+ matrix:
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+ python-version:
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+ - '3.11'
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+ - '3.12'
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+ - '3.13'
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+ - '3.14'
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+ steps:
56
+ - name: 'Install just'
57
+ uses: 'extractions/setup-just@v3'
58
+ - name: 'Checkout repository'
59
+ uses: 'actions/checkout@v6'
60
+ with:
61
+ persist-credentials: false
62
+ - name: 'Setup uv with python ${{ matrix.python-version }}'
63
+ uses: 'astral-sh/setup-uv@v7.2.0'
64
+ with:
65
+ enable-cache: true
66
+ cache-dependency-glob: 'pyproject.toml'
67
+ python-version: '${{ matrix.python-version }}'
68
+ - name: 'Run Checks'
69
+ run: 'just ci'
70
+ env:
71
+ UV_PYTHON_VERSION: '${{ matrix.python-version }}'
72
+ docs:
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+ name: 'Docs (${{ matrix.python-version }})'
74
+ runs-on: 'ubuntu-latest'
75
+ strategy:
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+ matrix:
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+ python-version:
78
+ - '3.12'
79
+ steps:
80
+ - name: 'Install just'
81
+ uses: 'extractions/setup-just@v3'
82
+ - name: 'Checkout repository'
83
+ uses: 'actions/checkout@v6'
84
+ with:
85
+ persist-credentials: false
86
+ - name: 'Setup uv'
87
+ uses: 'astral-sh/setup-uv@v7.2.0'
88
+ with:
89
+ enable-cache: true
90
+ cache-dependency-glob: 'pyproject.toml'
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+ python-version: '${{ matrix.python-version }}'
92
+ - name: 'Build Documentation'
93
+ run: 'just docs'
94
+ env:
95
+ UV_PYTHON_VERSION: '${{ matrix.python-version }}'
@@ -0,0 +1,108 @@
1
+ ---
2
+ name: 'GitHub Pages Documentation'
3
+
4
+ 'on':
5
+ push:
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+ branches:
7
+ - 'main'
8
+ workflow_call:
9
+ inputs:
10
+ deploy-mode:
11
+ description: 'Deployment mode used to determine docs aliases'
12
+ required: false
13
+ default: 'push'
14
+ type: 'string'
15
+ workflow_dispatch:
16
+ inputs:
17
+ deploy-mode:
18
+ description: 'Deployment mode used to determine docs aliases'
19
+ required: false
20
+ default: 'push'
21
+ type: 'choice'
22
+ options:
23
+ - 'push'
24
+ - 'release'
25
+
26
+ concurrency:
27
+ group: ${{ github.workflow }}-${{ github.ref }}
28
+ cancel-in-progress: true
29
+
30
+ permissions:
31
+ contents: 'read'
32
+
33
+ jobs:
34
+ deploy:
35
+ name: 'Deploy Documentation to GitHub Pages'
36
+ runs-on: 'ubuntu-latest'
37
+ strategy:
38
+ matrix:
39
+ python-version:
40
+ - '3.12'
41
+ permissions:
42
+ contents: 'write' # Needed to push to gh-pages
43
+ steps:
44
+ - name: 'Install just'
45
+ uses: 'extractions/setup-just@v3'
46
+ - name: 'Checkout repository'
47
+ uses: 'actions/checkout@v6'
48
+ with:
49
+ ref: 'main'
50
+ persist-credentials: true
51
+ - name: 'Fetch gh-pages branch'
52
+ run: |
53
+ git fetch origin gh-pages:gh-pages --depth=1
54
+ git config --global user.name "${ACTOR}"
55
+ git config --global user.email "${ACTOR}@users.noreply.github.com"
56
+ env:
57
+ ACTOR: "${{ github.actor }}"
58
+ - name: 'Setup uv with python ${{ matrix.python-version }}'
59
+ uses: 'astral-sh/setup-uv@v7.2.0'
60
+ with:
61
+ enable-cache: true
62
+ cache-dependency-glob: 'pyproject.toml'
63
+ python-version: '${{ matrix.python-version }}'
64
+ - name: 'Extract op_engine version'
65
+ id: extract-version
66
+ run: |
67
+ cat > version.py << EOF
68
+ import tomllib
69
+ with open('pyproject.toml', 'rb') as f:
70
+ data = tomllib.load(f)
71
+ version = data['project']['version']
72
+ version = '.'.join(version.split('.')[:2])
73
+ print(f"version={version}")
74
+ EOF
75
+ uv run -qq python version.py >> $GITHUB_OUTPUT
76
+ rm version.py
77
+ - name: 'Build API Reference'
78
+ run: 'just api-reference'
79
+ - name: 'Determine deploy mode'
80
+ id: determine-mode
81
+ run: |
82
+ if [ "${EVENT_NAME}" = "workflow_call" ]; then
83
+ echo "deploy-mode=${CALL_MODE}" >> "${GITHUB_OUTPUT}"
84
+ elif [ "${EVENT_NAME}" = "workflow_dispatch" ] \
85
+ && [ -n "${DISPATCH_MODE}" ]; then
86
+ echo "deploy-mode=${DISPATCH_MODE}" >> "${GITHUB_OUTPUT}"
87
+ else
88
+ echo "deploy-mode=push" >> "${GITHUB_OUTPUT}"
89
+ fi
90
+ env:
91
+ CALL_MODE: '${{ inputs.deploy-mode }}'
92
+ DISPATCH_MODE: '${{ github.event.inputs.deploy-mode }}'
93
+ EVENT_NAME: '${{ github.event_name }}'
94
+ - name: 'Deploy to GitHub Pages'
95
+ run: |
96
+ uv run mike set-default latest
97
+ if [ "${DEPLOY_MODE}" = "release" ] || [[ $VERSION == 0* ]]; then
98
+ ALIAS=latest
99
+ else
100
+ ALIAS=dev
101
+ fi
102
+ uv run mike deploy \
103
+ --push --update-aliases \
104
+ ${VERSION} ${ALIAS}
105
+ env:
106
+ DEPLOY_MODE: "${{ steps.determine-mode.outputs.deploy-mode }}"
107
+ GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
108
+ VERSION: "${{ steps.extract-version.outputs.version }}"
@@ -0,0 +1,194 @@
1
+ ---
2
+ name: 'Release'
3
+
4
+ 'on':
5
+ workflow_dispatch:
6
+ inputs:
7
+ publish-target:
8
+ description: 'Package publish target'
9
+ required: true
10
+ default: 'none'
11
+ type: 'choice'
12
+ options:
13
+ - 'none'
14
+ - 'testpypi'
15
+ - 'pypi'
16
+ create-github-release:
17
+ description: 'Create the GitHub release after publishing'
18
+ required: true
19
+ default: false
20
+ type: 'boolean'
21
+ deploy-docs:
22
+ description: 'Deploy versioned docs after creating the GitHub release'
23
+ required: true
24
+ default: false
25
+ type: 'boolean'
26
+
27
+ permissions:
28
+ contents: 'read'
29
+
30
+ jobs:
31
+ validate:
32
+ name: 'Validate release'
33
+ runs-on: 'ubuntu-latest'
34
+ outputs:
35
+ version: '${{ steps.validate-version.outputs.version }}'
36
+ docs-version: '${{ steps.validate-version.outputs.docs-version }}'
37
+ prerelease: '${{ steps.validate-version.outputs.prerelease }}'
38
+ steps:
39
+ - name: 'Install just'
40
+ uses: 'extractions/setup-just@v3'
41
+ - name: 'Checkout repository'
42
+ uses: 'actions/checkout@v6'
43
+ with:
44
+ fetch-depth: 0
45
+ persist-credentials: false
46
+ - name: 'Setup uv with python 3.12'
47
+ uses: 'astral-sh/setup-uv@v7.2.0'
48
+ with:
49
+ enable-cache: true
50
+ cache-dependency-glob: |
51
+ pyproject.toml
52
+ flepimop2-op_engine/pyproject.toml
53
+ python-version: '3.12'
54
+ - name: 'Validate shared package version'
55
+ id: validate-version
56
+ run: 'uv run python scripts/release_validate.py --github-output "${GITHUB_OUTPUT}"'
57
+ - name: 'Run release build validation'
58
+ run: 'just build-all'
59
+ env:
60
+ UV_PYTHON_VERSION: '3.12'
61
+ - name: 'Build core release artifacts'
62
+ run: |
63
+ rm -rf release-dist
64
+ mkdir -p release-dist/op_engine
65
+ uv run --with build --with twine python -m build --outdir release-dist/op_engine
66
+ uv run --with twine python -m twine check --strict release-dist/op_engine/*
67
+ - name: 'Build provider release artifacts'
68
+ run: |
69
+ mkdir -p release-dist/flepimop2-op_engine
70
+ cd flepimop2-op_engine
71
+ uv run --with build --with twine python -m build --outdir ../release-dist/flepimop2-op_engine
72
+ uv run --with twine python -m twine check --strict ../release-dist/flepimop2-op_engine/*
73
+ - name: 'Upload core package artifacts'
74
+ uses: 'actions/upload-artifact@v7'
75
+ with:
76
+ name: 'op-engine-dist'
77
+ path: 'release-dist/op_engine/*'
78
+ if-no-files-found: 'error'
79
+ - name: 'Upload provider package artifacts'
80
+ uses: 'actions/upload-artifact@v7'
81
+ with:
82
+ name: 'flepimop2-op-engine-dist'
83
+ path: 'release-dist/flepimop2-op_engine/*'
84
+ if-no-files-found: 'error'
85
+
86
+ publish-core:
87
+ name: 'Publish op_engine'
88
+ needs:
89
+ - 'validate'
90
+ runs-on: 'ubuntu-latest'
91
+ permissions:
92
+ id-token: 'write'
93
+ steps:
94
+ - name: 'Skip core publish'
95
+ if: "${{ github.event.inputs.publish-target == 'none' }}"
96
+ run: 'echo "publish-target=none; skipping op_engine publish."'
97
+ - name: 'Download core package artifacts'
98
+ if: "${{ github.event.inputs.publish-target != 'none' }}"
99
+ uses: 'actions/download-artifact@v8'
100
+ with:
101
+ name: 'op-engine-dist'
102
+ path: 'dist'
103
+ - name: 'Publish core package to TestPyPI'
104
+ if: "${{ github.event.inputs.publish-target == 'testpypi' }}"
105
+ uses: 'pypa/gh-action-pypi-publish@release/v1'
106
+ with:
107
+ packages-dir: 'dist'
108
+ repository-url: 'https://test.pypi.org/legacy/'
109
+ - name: 'Publish core package to PyPI'
110
+ if: "${{ github.event.inputs.publish-target == 'pypi' }}"
111
+ uses: 'pypa/gh-action-pypi-publish@release/v1'
112
+ with:
113
+ packages-dir: 'dist'
114
+
115
+ publish-provider:
116
+ name: 'Publish flepimop2-op_engine'
117
+ needs:
118
+ - 'validate'
119
+ - 'publish-core'
120
+ runs-on: 'ubuntu-latest'
121
+ permissions:
122
+ id-token: 'write'
123
+ steps:
124
+ - name: 'Skip provider publish'
125
+ if: "${{ github.event.inputs.publish-target == 'none' }}"
126
+ run: 'echo "publish-target=none; skipping flepimop2-op_engine publish."'
127
+ - name: 'Download provider package artifacts'
128
+ if: "${{ github.event.inputs.publish-target != 'none' }}"
129
+ uses: 'actions/download-artifact@v8'
130
+ with:
131
+ name: 'flepimop2-op-engine-dist'
132
+ path: 'dist'
133
+ - name: 'Publish provider package to TestPyPI'
134
+ if: "${{ github.event.inputs.publish-target == 'testpypi' }}"
135
+ uses: 'pypa/gh-action-pypi-publish@release/v1'
136
+ with:
137
+ packages-dir: 'dist'
138
+ repository-url: 'https://test.pypi.org/legacy/'
139
+ - name: 'Publish provider package to PyPI'
140
+ if: "${{ github.event.inputs.publish-target == 'pypi' }}"
141
+ uses: 'pypa/gh-action-pypi-publish@release/v1'
142
+ with:
143
+ packages-dir: 'dist'
144
+
145
+ create-github-release:
146
+ name: 'Create GitHub release'
147
+ needs:
148
+ - 'validate'
149
+ - 'publish-provider'
150
+ if: >-
151
+ ${{
152
+ github.event.inputs.create-github-release == 'true' &&
153
+ (github.event.inputs.publish-target == 'none' ||
154
+ needs.publish-provider.result == 'success')
155
+ }}
156
+ runs-on: 'ubuntu-latest'
157
+ permissions:
158
+ contents: 'write'
159
+ steps:
160
+ - name: 'Create release'
161
+ run: |
162
+ ARGS=(
163
+ release create "v${VERSION}"
164
+ --repo "${GITHUB_REPOSITORY}"
165
+ --target "${GITHUB_SHA}"
166
+ --title "v${VERSION}"
167
+ --generate-notes
168
+ )
169
+ if [ "${PRERELEASE}" = 'true' ]; then
170
+ ARGS+=(--prerelease)
171
+ fi
172
+ gh "${ARGS[@]}"
173
+ env:
174
+ GH_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
175
+ GITHUB_REPOSITORY: '${{ github.repository }}'
176
+ GITHUB_SHA: '${{ github.sha }}'
177
+ PRERELEASE: '${{ needs.validate.outputs.prerelease }}'
178
+ VERSION: '${{ needs.validate.outputs.version }}'
179
+
180
+ deploy-docs:
181
+ name: 'Deploy release docs'
182
+ needs:
183
+ - 'create-github-release'
184
+ if: >-
185
+ ${{
186
+ github.event.inputs.deploy-docs == 'true' &&
187
+ needs.create-github-release.result == 'success'
188
+ }}
189
+ permissions:
190
+ contents: 'write'
191
+ uses: './.github/workflows/gh-pages.yaml'
192
+ with:
193
+ deploy-mode: 'release'
194
+ secrets: 'inherit'
@@ -0,0 +1,187 @@
1
+ # ================================
2
+ # Python bytecode / cache
3
+ # ================================
4
+ __pycache__/
5
+ *.py[codz]
6
+ *$py.class
7
+
8
+ # C extensions
9
+ *.so
10
+
11
+ # ================================
12
+ # Distribution / packaging
13
+ # ================================
14
+ .Python
15
+ build/
16
+ develop-eggs/
17
+ dist/
18
+ downloads/
19
+ eggs/
20
+ .eggs/
21
+ lib/
22
+ lib64/
23
+ parts/
24
+ sdist/
25
+ var/
26
+ wheels/
27
+ share/python-wheels/
28
+ *.egg-info/
29
+ .installed.cfg
30
+ *.egg
31
+ MANIFEST
32
+
33
+ # ================================
34
+ # PyInstaller
35
+ # ================================
36
+ *.manifest
37
+ *.spec
38
+
39
+ # ================================
40
+ # Logs / coverage / testing
41
+ # ================================
42
+ pip-log.txt
43
+ pip-delete-this-directory.txt
44
+
45
+ htmlcov/
46
+ .tox/
47
+ .nox/
48
+ .coverage
49
+ .coverage.*
50
+ .cache
51
+ nosetests.xml
52
+ coverage.xml
53
+ *.cover
54
+ *.py.cover
55
+ .hypothesis/
56
+ .pytest_cache/
57
+ cover/
58
+
59
+ # ================================
60
+ # Localization
61
+ # ================================
62
+ *.mo
63
+ *.pot
64
+
65
+ # ================================
66
+ # Framework-specific
67
+ # ================================
68
+ *.log
69
+ local_settings.py
70
+ db.sqlite3
71
+ db.sqlite3-journal
72
+
73
+ instance/
74
+ .webassets-cache
75
+ .scrapy
76
+
77
+ docs/_build/
78
+
79
+ .pybuilder/
80
+ target/
81
+
82
+ # ================================
83
+ # Jupyter / IPython
84
+ # ================================
85
+ .ipynb_checkpoints
86
+ profile_default/
87
+ ipython_config.py
88
+
89
+ # ================================
90
+ # Python env managers
91
+ # ================================
92
+ .python-version
93
+
94
+ # ================================
95
+ # Dependency managers
96
+ # ================================
97
+ uv.lock
98
+
99
+ .pdm-python
100
+ .pdm-build/
101
+
102
+ .pixi
103
+
104
+ __pypackages__/
105
+
106
+ # ================================
107
+ # Runtime artifacts
108
+ # ================================
109
+ celerybeat-schedule
110
+ celerybeat.pid
111
+
112
+ *.sage.py
113
+
114
+ # ================================
115
+ # Virtual environments
116
+ # ================================
117
+ .env
118
+ .envrc
119
+ .venv
120
+ env/
121
+ venv/
122
+ ENV/
123
+ env.bak/
124
+ venv.bak/
125
+
126
+ # ================================
127
+ # IDEs / Editors
128
+ # ================================
129
+ .vscode/
130
+ .spyderproject
131
+ .spyproject
132
+ .ropeproject
133
+
134
+ /site
135
+
136
+ .mypy_cache/
137
+ .dmypy.json
138
+ dmypy.json
139
+
140
+ .pyre/
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+ .pytype/
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+
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+ cython_debug/
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+
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+ .ruff_cache/
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+
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+ .pypirc
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+
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+ .cursorignore
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+ .cursorindexingignore
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+
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+ marimo/_static/
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+ marimo/_lsp/
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+ __marimo__/
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+
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+ # ================================
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+ # macOS / Apple filesystem junk
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+ # ================================
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+ .DS_Store
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+ .AppleDouble
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+ .LSOverride
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+ ._*
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+ .Spotlight-V100
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+ .Trashes
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+ .VolumeIcon.icns
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+ .fseventsd
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+ .Rhistory
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+
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+ # ================================
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+ # Example output artifacts
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+ # ================================
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+
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+ # Matplotlib / plotting outputs
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+ *.png
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+ *.pdf
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+ *.svg
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+
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+ # Numpy saved arrays
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+ *.npy
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+ *.npz
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+
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+ # CSV outputs from examples
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+ *.csv
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+
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+ # Optional example output directory convention
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+ examples/output/
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+
@@ -0,0 +1,19 @@
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+ Copyright (c) 2026 Joshua Macdonald, Carl Pearson, and Timothy Willard
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
8
+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.