lamindb 0.77.2__tar.gz → 1.0rc1__tar.gz

lamindb-1.0rc1/.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: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: dorny/paths-filter@v3
+        id: changes
+        if: github.event_name != 'push'
+        with:
+          filters: |
+            curator:
+              - 'lamindb/curators/**'
+              - 'tests/curators/test_curator.py'
+
+      - id: set-matrix
+        run: |
+          if [[ "${{ github.event_name }}" == "push" ]]; then
+            # On push, run all
+            echo "matrix={\"group\":[\"unit-core\",\"unit-storage\",\"tutorial\",\"guide\",\"biology\",\"faq\",\"storage\",\"cli\",\"curator\"]}" >> $GITHUB_OUTPUT
+          elif [[ "${{ steps.changes.outputs.curator }}" == "true" ]]; then
+            # If curator paths changed, include curator
+            echo "matrix={\"group\":[\"unit-core\",\"unit-storage\",\"tutorial\",\"guide\",\"biology\",\"faq\",\"storage\",\"cli\",\"curator\"]}" >> $GITHUB_OUTPUT
+          else
+            # Otherwise, run all except curator
+            echo "matrix={\"group\":[\"unit-core\",\"unit-storage\",\"tutorial\",\"guide\",\"biology\",\"faq\",\"storage\",\"cli\"]}" >> $GITHUB_OUTPUT
+          fi
+
+  test:
+    needs: pre-filter
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.pre-filter.outputs.matrix)}}
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: |
+            ${{ matrix.group == 'storage' && '3.10' ||
+                matrix.group == 'unit-storage' && '3.11' ||
+                '3.12' }}
+
+      - name: cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+
+      - name: cache postgres
+        if: ${{ matrix.group == 'faq' || matrix.group == 'unit-core' || matrix.group == 'unit-storage' }}
+        id: cache-postgres
+        uses: actions/cache@v4
+        with:
+          path: ~/postgres.tar
+          key: cache-postgres-0
+
+      - name: cache postgres miss
+        if: ${{ 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: ${{ steps.cache-postgres.outputs.cache-hit == 'true' }}
+        run: docker image load --input ~/postgres.tar
+
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+
+      - 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' }}
+        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: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - run: nox -s "build(group='${{ 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 }}
+
+  docs:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: checkout lndocs
+        uses: actions/checkout@v4
+        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: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
+      - run: nox -s "install_ci(group='docs')"
+      - uses: actions/download-artifact@v4
+      - run: nox -s docs
+      - uses: nwtgck/actions-netlify@v1.2
+        with:
+          publish-dir: "_build/html"
+          production-deploy: ${{ github.event_name == 'push' }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          enable-commit-comment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+      - 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@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - 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-1.0rc1/.gitignore

@@ -0,0 +1,215 @@
+__MACOSX/
+
+# LaminDB
+*.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/
+test-inherit1
+test-inherit2
+test-search0
+test-search1
+test-search5
+default_storage
+default_storage_unit_core
+default_storage_unit_storage
+test.ipynb
+run-tests
+test-django-validation/
+
+# 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
+
+# Pyre type checker
+.pyre/
+
+# data files
+data/
+_build
+*.csv
+*.fcs
+*.zip
+*.feather
+*.h5ad
+*.h5mu
+*.parquet
+*.bam
+*.fastq.gz
+*.pt
+
+# Pycharm
+.idea
+
+# VSCode
+.vscode

lamindb-1.0rc1/.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/wetlab"]
+	path = sub/wetlab
+	url = https://github.com/laminlabs/wetlab
+[submodule "sub/clinicore"]
+	path = sub/clinicore
+	url = https://github.com/laminlabs/clinicore

lamindb-1.0rc1/.pre-commit-config.yaml

@@ -0,0 +1,59 @@
+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/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
+    hooks:
+      - id: prettier
+        exclude: |
+          (?x)(
+            docs/changelog.md|.github/ISSUE_TEMPLATE/config.yml|tests/core/notebooks/basic-r-notebook.Rmd.cleaned.html
+          )
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/
+          )
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.6
+    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: v1.7.1
+  #   hooks:
+  #     - id: mypy
+  #       args: [--no-strict-optional, --ignore-missing-imports]
+  #       additional_dependencies: ["types-requests", "types-attrs"]
+  #       exclude: |
+  #         (?x)(
+  #             test_notebooks.py|script-to-test-versioning.py|tests/storage/conftest.py
+  #         )

lamindb-1.0rc1/PKG-INFO

@@ -0,0 +1,66 @@
+Metadata-Version: 2.3
+Name: lamindb
+Version: 1.0rc1
+Summary: A data framework for biology.
+Author-email: Lamin Labs <open-source@lamin.ai>
+Requires-Python: >=3.10,<3.13
+Description-Content-Type: text/markdown
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: lamin_utils==0.13.10
+Requires-Dist: lamin_cli==1.0.2
+Requires-Dist: lamindb_setup[aws]==1.0.1
+Requires-Dist: pyarrow
+Requires-Dist: typing_extensions!=4.6.0
+Requires-Dist: python-dateutil
+Requires-Dist: scipy<1.15.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: anndata>=0.8.0,<=0.11.3
+Requires-Dist: fsspec
+Requires-Dist: graphviz
+Requires-Dist: psycopg2-binary
+Requires-Dist: bionty==1.0.0 ; extra == "bionty"
+Requires-Dist: cellregistry ; extra == "cellregistry"
+Requires-Dist: clinicore==1.0.0 ; extra == "clinicore"
+Requires-Dist: line_profiler ; extra == "dev"
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: nox ; extra == "dev"
+Requires-Dist: laminci>=0.3 ; extra == "dev"
+Requires-Dist: pytest>=6.0 ; extra == "dev"
+Requires-Dist: coverage ; extra == "dev"
+Requires-Dist: pytest-cov ; extra == "dev"
+Requires-Dist: mudata ; extra == "dev"
+Requires-Dist: nbproject_test>=0.6.0 ; extra == "dev"
+Requires-Dist: faker-biology ; extra == "dev"
+Requires-Dist: django-schema-graph ; extra == "erdiagram"
+Requires-Dist: readfcs>=1.1.9 ; extra == "fcs"
+Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
+Requires-Dist: nbproject==0.10.5 ; extra == "jupyter"
+Requires-Dist: jupytext ; extra == "jupyter"
+Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
+Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
+Requires-Dist: omop ; extra == "omop"
+Requires-Dist: wetlab==1.0.1 ; extra == "wetlab"
+Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
+Project-URL: Home, https://github.com/laminlabs/lamindb
+Provides-Extra: bionty
+Provides-Extra: cellregistry
+Provides-Extra: clinicore
+Provides-Extra: dev
+Provides-Extra: erdiagram
+Provides-Extra: fcs
+Provides-Extra: gcp
+Provides-Extra: jupyter
+Provides-Extra: omop
+Provides-Extra: wetlab
+Provides-Extra: zarr
+
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+
+# LaminDB - A data framework for biology
+
+Read the [docs](https://docs.lamin.ai).
+

lamindb-1.0rc1/docs/api.md

@@ -0,0 +1,33 @@
+# API
+
+<meta http-equiv="Refresh" content="0; url=./lamindb.html" />
+
+```{toctree}
+:maxdepth: 1
+:caption: CLI & lamindb
+:hidden:
+
+cli
+lamindb
+```
+
+```{toctree}
+:maxdepth: 1
+:caption: R & REST
+:hidden:
+
+laminr
+rest
+```
+
+```{toctree}
+:maxdepth: 1
+:caption: Modules
+:hidden:
+
+bionty
+wetlab
+clinicore
+cellregistry
+omop
+```