lamindb-core 2.3.0__tar.gz

lamindb_core-2.3.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Report a bug
+description: Report a bug.
+labels:
+  - ":bug: bug"
+body:
+  - type: textarea
+    id: report
+    attributes:
+      label: Add a description
+      placeholder: |
+        Describe and consider providing version information. Please ensure you're on the latest version of lamindb.
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true

lamindb_core-2.3.0/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true
+contact_links:
+    - name: LaminHub issues
+      url: https://github.com/laminlabs/laminhub-public
+      about: If you have issues with the GUI/web app at lamin.ai, please report them here.
+    - name: Enterprise support
+      url: https://lamin.ai/contact
+      about: If you have other questions, contact us directly.

lamindb_core-2.3.0/.github/ISSUE_TEMPLATE/enhancement.yml

@@ -0,0 +1,12 @@
+name: Propose an enhancement
+description: Propose an enhancement.
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Add a description
+      placeholder: |
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true

lamindb_core-2.3.0/.github/ISSUE_TEMPLATE/usage_question.yml

@@ -0,0 +1,14 @@
+name: Ask a usage question
+description: Ask a usage question.
+labels:
+  - "usage question"
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Add a description
+      placeholder: |
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true

lamindb_core-2.3.0/.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches: [release]
+  pull_request:
+
+jobs:
+  pre-filter:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: dorny/paths-filter@v3
+        id: changes
+        if: github.event_name != 'push'
+        with:
+          filters: |
+            curator:
+              - 'lamindb/curators/**'
+              - 'lamindb/examples/cellxgene/**'
+              - 'tests/curators/**'
+            integrations:
+              - 'lamindb/integrations/**'
+              - 'tests/integrations/**'
+
+      - id: set-matrix
+        shell: bash
+        run: |
+          BASE_GROUPS=$(jq -n -c '["unit-core-sqlite", "unit-core-postgres", "unit-storage", "tutorial", "guide", "biology", "faq", "storage", "cli", "permissions", "no-instance"]')
+          ADDITIONAL_GROUPS=[]
+
+          if [[ "${{ github.event_name }}" == "push" || "${{ github.event_name }}" == "repository_dispatch" ]]; then
+            # Run everything on push and dispatch
+            ADDITIONAL_GROUPS=$(jq -n -c '["curator", "integrations"]')
+          else
+            # Otherwise check which paths changed
+            if [[ "${{ steps.changes.outputs.curator }}" == "true" ]]; then
+              ADDITIONAL_GROUPS=$(jq -n -c --argjson groups "$ADDITIONAL_GROUPS" '$groups + ["curator"]')
+            fi
+            if [[ "${{ steps.changes.outputs.integrations }}" == "true" ]]; then
+              ADDITIONAL_GROUPS=$(jq -n -c --argjson groups "$ADDITIONAL_GROUPS" '$groups + ["integrations"]')
+            fi
+          fi
+
+          # Combine base groups with any additional groups
+          MATRIX=$(jq -n -c --argjson base "$BASE_GROUPS" --argjson additional "$ADDITIONAL_GROUPS" '{group: ($base + $additional)}')
+
+          # Output as single line for GitHub Actions
+          echo "matrix=$(echo "$MATRIX" | jq -c .)" >> $GITHUB_OUTPUT
+
+          # Pretty print for debugging
+          echo "Generated matrix:"
+          echo "$MATRIX" | jq .
+
+  test:
+    needs: pre-filter
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.pre-filter.outputs.matrix)}}
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - uses: actions/checkout@v6
+        if: ${{ matrix.group == 'permissions' }}
+        with:
+          repository: laminlabs/laminhub
+          token: ${{ secrets.GH_TOKEN_DEPLOY_LAMINAPP }}
+          path: laminhub
+          ref: main
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: |
+            ${{ github.ref == 'refs/heads/release' && '3.11' ||
+                '3.13'
+                }}
+
+      - name: cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: cache postgres
+        if: ${{ matrix.group == 'faq' || matrix.group == 'unit-core-postgres' || matrix.group == 'unit-storage' || matrix.group == 'permissions'}}
+        id: cache-postgres
+        uses: actions/cache@v4
+        with:
+          path: ~/postgres.tar
+          key: cache-postgres-0
+          restore-keys: |
+            cache-postgres-
+      - name: cache postgres miss
+        if: ${{ (matrix.group == 'faq' || matrix.group == 'unit-core-postgres' || matrix.group == 'unit-storage' || matrix.group == 'permissions') && steps.cache-postgres.outputs.cache-hit != 'true' }}
+        run: docker pull postgres:latest && docker image save postgres:latest --output ~/postgres.tar
+      - name: cache postgres use
+        if: ${{ (matrix.group == 'faq' || matrix.group == 'unit-core-postgres' || matrix.group == 'unit-storage' || matrix.group == 'permissions') && steps.cache-postgres.outputs.cache-hit == 'true' }}
+        run: docker image load --input ~/postgres.tar
+
+      - run: pip install "laminci@git+https://github.com/laminlabs/laminci"
+
+      - run: nox -s configure_coverage -- '${{needs.pre-filter.outputs.matrix}}'
+
+      - name: install postgres
+        if: ${{ matrix.group == 'faq' }}
+        run: sudo apt-get install libpq-dev
+
+      - name: install graphviz
+        if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq'}}
+        run: sudo apt-get -y install graphviz
+
+      # - run: nox -s lint
+      #   if: ${{ matrix.group == 'tutorial' }}
+
+      - run: nox -s "install_ci(group='${{ matrix.group }}')"
+
+      - uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - run: nox -s prepare
+        if: ${{ !startsWith(matrix.group, 'unit-') && !startsWith(matrix.group, 'permissions') }}
+      - run: nox -s "test(group='${{ matrix.group }}')"
+
+      - name: upload coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage--${{ matrix.group }}
+          path: .coverage
+          include-hidden-files: true
+
+      - name: upload docs
+        if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq' || matrix.group == 'storage' }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-${{ matrix.group }}
+          path: ./docs/${{ matrix.group }}
+
+  profile:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    env:
+      LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: |
+            ${{ github.ref == 'refs/heads/release' && '3.11' ||
+                '3.13'
+                }}
+      - run: pip install git+https://github.com/laminlabs/laminci
+      - run: nox -s "install_ci(group='unit-core-sqlite')"
+      - run: uv pip install --system git+https://github.com/laminlabs/laminprofiler
+      - run: lamin login
+      - run: laminprofiler check tests/profiling/import_lamindb_and_connect.py --threshold 3.5
+      - run: lamin connect laminlabs/lamindata
+      - run: laminprofiler check tests/profiling/import_lamindb.py --threshold 1.5
+
+  docs:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: checkout lndocs
+        uses: actions/checkout@v6
+        with:
+          repository: laminlabs/lndocs
+          ssh-key: ${{ secrets.READ_LNDOCS }}
+          path: lndocs
+          ref: main
+
+      - uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      - run: nox -s "install_ci(group='docs')"
+      - uses: actions/download-artifact@v4
+      - run: nox -s clidocs
+      - run: nox -s prepare
+      - run: nox -s docs
+      - run: rm -r ./_build/html/.doctrees # do not want to deploy with cloudflare
+      - uses: cloudflare/wrangler-action@v3
+        id: cloudflare
+        with:
+          apiToken: ${{ secrets.CLOUDFLARE_API_TOKEN }}
+          accountId: 472bdad691b4483dea759eadb37110bd
+          command: pages deploy "_build/html" --project-name=lamindb
+          gitHubToken: ${{ secrets.GITHUB_TOKEN }}
+      - uses: edumserrano/find-create-or-update-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          body-includes: "Deployment URL"
+          comment-author: "github-actions[bot]"
+          body: |
+            Deployment URL: ${{ steps.cloudflare.outputs.deployment-url }}
+          edit-mode: replace
+
+      - uses: peter-evans/repository-dispatch@v2
+        if: ${{ github.event_name == 'push' }}
+        with:
+          token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          repository: "laminlabs/lamin-docs"
+          event-type: build
+
+  coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+      - run: |
+          python -m pip install -U uv
+          uv pip install --system coverage[toml]
+          uv pip install --system --no-deps .
+
+      - uses: actions/download-artifact@v4
+      - name: run coverage
+        run: |
+          coverage combine coverage--*/.coverage*
+          coverage report --fail-under=0
+          coverage xml
+      - uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  dispatch:
+    if: ${{ github.event_name == 'push' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: peter-evans/repository-dispatch@v2
+        with:
+          token: ${{ secrets.LAMIN_BUILD_DOCS }}
+          repository: "laminlabs/lamindb-dispatch"
+          event-type: build

lamindb_core-2.3.0/.github/workflows/doc-changes.yml

@@ -0,0 +1,24 @@
+name: doc-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+      - release
+    types:
+      - closed
+
+jobs:
+  doc-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

lamindb_core-2.3.0/.gitignore

@@ -0,0 +1,243 @@
+__MACOSX/
+
+# LaminDB
+README_stripped.md
+docs/scripts/test_artifact_parquet.py
+README.ipynb
+docs/sample.fasta
+docs/faq/sample.fasta
+docs/faq/test-acid/
+docs/scripts/define_mini_immuno_features_labels.py
+docs/scripts/define_mini_immuno_schema_flexible.py
+docs/scripts/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
+docs/scripts/define_valid_features.py
+docs/scripts/save_mini_immuno_datasets.py
+profile_output*
+docs/cli.md
+.coveragerc
+*.db
+*.lndb
+*.jpg
+*.zarr/
+docsbuild/
+docs/lamin.md
+docs/guide/data-validation.ipynb
+docs/guide/bionty.ipynb
+docs/guide/lnschema-core.ipynb
+docs/paradisi05_laminopathic_nuclei.jpg
+bionty_docs/
+lamindb_docs/
+_build
+mydata/
+lamin-intro/
+lamin-tutorial/
+mytest/
+rds/
+mydb/
+docs/test-registries/
+docs/test-annotate-flexible/
+docs/lamindb.*
+lamin_sphinx
+docs/conf.py
+lamindb/setup/.env
+_secrets.py
+_configuration.py
+lamin.db
+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/
+docs/test-annotate/
+docs/test-track/
+suo22/
+docs/biology/test-flow/
+docs/biology/test-scrna/
+docs/biology/test-registries/
+docs/biology/test-multimodal/
+default_storage
+default_storage_unit_core
+default_storage_unit_storage
+test.ipynb
+test2.ipynb
+run-tests
+test-django-validation/
+curate.tiledbsoma
+small_dataset.tiledbsoma
+nonregistered_storage
+registered_storage
+tests/core/notebooks/no-uid-renamed.ipynb
+
+# General
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+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
+*.pt
+
+# Pycharm
+.idea
+
+# VSCode
+.vscode
+
+# CELLxGENE
+!lamindb/examples/cellxgene/cellxgene_schema_versions.csv
+
+# ml
+lightning_logs
+mlruns
+download_mnist
+checkpoints
+test_lightning

lamindb_core-2.3.0/.gitmodules

@@ -0,0 +1,15 @@
+[submodule "sub/lamindb-setup"]
+	path = sub/lamindb-setup
+	url = https://github.com/laminlabs/lamindb-setup
+[submodule "sub/lamin-cli"]
+	path = sub/lamin-cli
+	url = https://github.com/laminlabs/lamin-cli
+[submodule "sub/bionty"]
+	path = sub/bionty
+	url = https://github.com/laminlabs/bionty
+[submodule "sub/pertdb"]
+	path = sub/pertdb
+	url = https://github.com/laminlabs/pertdb
+[submodule "sub/cellxgene-lamin"]
+	path = sub/cellxgene-lamin
+	url = https://github.com/laminlabs/cellxgene-lamin.git

lamindb_core-2.3.0/.pre-commit-config.yaml

@@ -0,0 +1,75 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.5.1
+    hooks:
+      - id: prettier
+        exclude: |
+          (?x)(
+            docs/changelog.md|.github/ISSUE_TEMPLATE/config.yml|tests/core/notebooks/basic-r-notebook.Rmd.cleaned.html|README.md
+          )
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/
+          )
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.10
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+            )
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+        exclude: |
+          (?x)(
+              tests/core/notebooks/basic-r-notebook.Rmd.cleaned.html
+            )
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        args:
+          [
+            --no-strict-optional,
+            --ignore-missing-imports,
+            --disable-error-code=annotation-unchecked,
+            --disable-error-code=type-arg,
+          ]
+        additional_dependencies:
+          ["types-requests", "types-attrs", "types-PyYAML"]
+        exclude: |
+          (?x)(
+              test_notebooks.py|
+              script-to-test-versioning.py|
+              tests/storage/conftest.py|
+              tests/curators/conftest.py|
+              tests/permissions/conftest.py|
+              tests/writelog/conftest.py|
+              tests/writelog_sqlite/conftest.py|
+              tests/curators/test_curators_examples.py|
+              tests/core/conftest.py|
+              docs/scripts/
+          )