lamin_cli 1.11.0__tar.gz → 1.12.1__tar.gz

{lamin_cli-1.11.0 → lamin_cli-1.12.1}/.github/workflows/build.yml

@@ -1,82 +1,73 @@
-name: build
-
-on:
-  push:
-    branches: [release]
-  pull_request:
-
-jobs:
-  pre-filter:
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.set-matrix.outputs.matrix }}
-    steps:
-      - uses: actions/checkout@v5
-        with:
-          fetch-depth: 0
-
-      - uses: dorny/paths-filter@v3
-        id: changes
-        if: github.event_name != 'push'
-        with:
-          filters: |
-            modal:
-              - 'lamin_cli/compute/modal.py'
-              - 'tests/modal/**'
-
-      - id: set-matrix
-        shell: bash
-        run: |
-          BASE_GROUPS=$(jq -n -c '[]')
-
-          if [[ "${{ github.event_name }}" == "push" || "${{ steps.changes.outputs.modal }}" == "true" ]]; then
-            # Run everything on push or when modal paths change
-            MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: ($groups + ["modal"])}')
-          else
-            # Otherwise only run base groups
-            MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: $groups}')
-          fi
-
-          # Output as single line for GitHub Actions
-          echo "matrix=$(echo "$MATRIX" | jq -c .)" >> $GITHUB_OUTPUT
-
-          # Pretty print for debugging
-          echo "Generated matrix:"
-          echo "$MATRIX" | jq .
-
-  test:
-    needs: pre-filter
-    runs-on: ubuntu-latest
-    env:
-      LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }}
-    strategy:
-      fail-fast: false
-      matrix: ${{fromJson(needs.pre-filter.outputs.matrix)}}
-    timeout-minutes: 20
-    steps:
-      - uses: actions/checkout@v5
-        with:
-          submodules: recursive
-          fetch-depth: 0
-
-      - uses: actions/setup-python@v6
-        with:
-          python-version: 3.12
-
-      - name: cache pre-commit
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
-
-      - run: pip install git+https://github.com/laminlabs/laminci
-
-      - run: uv pip install --system modal pytest
-
-      - run: modal token set --token-id ${{ secrets.MODAL_DEV_TOKEN_ID }} --token-secret ${{ secrets.MODAL_DEV_TOKEN_SECRET }}
-
-      - run: nox -s setup
-
-      - run: lamin login
-
-      - run: pytest tests/modal
+name: build
+
+on:
+  push:
+    branches: [release, main]
+  pull_request:
+
+jobs:
+  pre-filter:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+      has_groups: ${{ steps.set-matrix.outputs.has_groups }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+      - uses: dorny/paths-filter@v3
+        id: changes
+        if: github.event_name != 'push'
+        with:
+          filters: |
+            modal:
+              - 'lamin_cli/compute/modal.py'
+              - 'tests/modal/**'
+      - id: set-matrix
+        shell: bash
+        run: |
+          BASE_GROUPS=$(jq -n -c '[]')
+          # Run everything on push or when modal paths change
+          if [[ "${{ github.event_name }}" == "push" || "${{ steps.changes.outputs.modal }}" == "true" ]]; then
+            MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: ($groups + ["modal"])}')
+            echo "has_groups=true" >> $GITHUB_OUTPUT
+          # Otherwise only run base groups
+          else
+            MATRIX=$(jq -n -c --argjson groups "$BASE_GROUPS" '{group: $groups}')
+            echo "has_groups=false" >> $GITHUB_OUTPUT
+          fi
+          # Output as single line for GitHub Actions
+          echo "matrix=$(echo "$MATRIX" | jq -c .)" >> $GITHUB_OUTPUT
+          # Pretty print for debugging
+          echo "Generated matrix:"
+          echo "$MATRIX" | jq .
+
+  test:
+    needs: pre-filter
+    if: needs.pre-filter.outputs.has_groups == 'true'
+    runs-on: ubuntu-latest
+    env:
+      LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }}
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.pre-filter.outputs.matrix)}}
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.12
+      - name: cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+      - run: pip install git+https://github.com/laminlabs/laminci
+      - run: uv pip install --system modal pytest
+      - run: modal token set --token-id ${{ secrets.MODAL_DEV_TOKEN_ID }} --token-secret ${{ secrets.MODAL_DEV_TOKEN_SECRET }}
+      - run: nox -s setup
+      - run: lamin login
+      - run: pytest tests/modal

{lamin_cli-1.11.0 → lamin_cli-1.12.1}/.github/workflows/doc-changes.yml

@@ -1,23 +1,23 @@
-name: doc-changes
-
-on:
-  pull_request_target:
-    branches:
-      - main
-    types:
-      - closed
-
-jobs:
-  latest-changes:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-      - run: pip install "laminci[doc-changes]@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
-      - run: laminci doc-changes
-        env:
-          repo_token: ${{ secrets.GITHUB_TOKEN }}
-          docs_token: ${{ secrets.LAMIN_BUILD_DOCS }}
-          changelog_file: lamin-docs/docs/changelog/soon/lamindb.md
+name: doc-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    types:
+      - closed
+
+jobs:
+  latest-changes:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: pip install "laminci[doc-changes]@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      - run: laminci doc-changes
+        env:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          docs_token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          changelog_file: lamin-docs/docs/changelog/soon/lamindb.md

{lamin_cli-1.11.0 → lamin_cli-1.12.1}/.gitignore

@@ -1,195 +1,196 @@
-# LaminDB
-modal_mount_dir/
-lamindb_docs/
-_build
-mydata/
-lamin-intro/
-lamin-tutorial/
-mytest/
-rds/
-mydb/
-bfx-output/
-scrnaseq-cellranger/
-scrnaseq-cellranger-schmidt22/
-cellranger_run_001
-__MACOSX/
-docs/lamindb.*
-lamin_sphinx
-docs/conf.py
-*.db
-*.lndb
-*.zarr/
-lamindb/setup/.env
-_secrets.py
-_configuration.py
-docs/generated/*
-_docs_tmp*
-docs/guide/Laminopathic_nuclei.jpg
-docs/guide/paradisi05_laminopathic_nuclei.jpg
-nocodb
-docs/guide/SRR4238351_subsamp.fastq.gz
-docs/faq/paradisi05_laminopathic_nuclei.jpg
-docs/faq/tostore/
-docs/faq/mydata_postgres/
-docs/guide/myobjects/
-docs/faq/test-run-inputs/
-docs/intro/paradisi05_laminopathic_nuclei.jpg
-docs/guide/figures/
-suo22/
-docs/biology/test-flow/
-docs/biology/test-scrna/
-docs/biology/test-registries/
-docs/biology/test-multimodal/
-test.ipynb
-
-# General
-.DS_Store
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-caches/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# ruff
-.ruff_cache
-
-# Pyre type checker
-.pyre/
-
-# data files
-data/
-_build
-*.csv
-*.fcs
-*.zip
-*.feather
-*.h5ad
-*.h5mu
-*.parquet
-*.bam
-*.fastq.gz
-
-# Pycharm
-.idea
+# LaminDB
+tests/core/tmp_cache_test/
+modal_mount_dir/
+lamindb_docs/
+_build
+mydata/
+lamin-intro/
+lamin-tutorial/
+mytest/
+rds/
+mydb/
+bfx-output/
+scrnaseq-cellranger/
+scrnaseq-cellranger-schmidt22/
+cellranger_run_001
+__MACOSX/
+docs/lamindb.*
+lamin_sphinx
+docs/conf.py
+*.db
+*.lndb
+*.zarr/
+lamindb/setup/.env
+_secrets.py
+_configuration.py
+docs/generated/*
+_docs_tmp*
+docs/guide/Laminopathic_nuclei.jpg
+docs/guide/paradisi05_laminopathic_nuclei.jpg
+nocodb
+docs/guide/SRR4238351_subsamp.fastq.gz
+docs/faq/paradisi05_laminopathic_nuclei.jpg
+docs/faq/tostore/
+docs/faq/mydata_postgres/
+docs/guide/myobjects/
+docs/faq/test-run-inputs/
+docs/intro/paradisi05_laminopathic_nuclei.jpg
+docs/guide/figures/
+suo22/
+docs/biology/test-flow/
+docs/biology/test-scrna/
+docs/biology/test-registries/
+docs/biology/test-multimodal/
+test.ipynb
+
+# General
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+caches/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache
+
+# Pyre type checker
+.pyre/
+
+# data files
+data/
+_build
+*.csv
+*.fcs
+*.zip
+*.feather
+*.h5ad
+*.h5mu
+*.parquet
+*.bam
+*.fastq.gz
+
+# Pycharm
+.idea

{lamin_cli-1.11.0 → lamin_cli-1.12.1}/.pre-commit-config.yaml

@@ -1,40 +1,40 @@
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-        exclude: |
-          (?x)(
-              .github/workflows/latest-changes.jinja2
-          )
-      - id: check-yaml
-      - id: check-added-large-files
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.6
-    hooks:
-      - id: ruff-check
-        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
-      - id: ruff-format
-  - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.6.2
-    hooks:
-      - id: prettier
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
-    hooks:
-      - id: nbstripout
-        exclude: |
-          (?x)(
-              docs/examples/|
-              docs/notes/|
-              tests
-          )
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
-    hooks:
-      - id: mypy
-        exclude: |
-          (?x)(
-              tests/hub-local/conftest.py
-          )
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+          )
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.6
+    hooks:
+      - id: ruff-check
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.6.2
+    hooks:
+      - id: prettier
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.3.9
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/|
+              tests
+          )
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.2
+    hooks:
+      - id: mypy
+        exclude: |
+          (?x)(
+              tests/hub-local/conftest.py
+          )