lamindb 0.76.7__tar.gz → 0.76.8__tar.gz

lamindb-0.76.8/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report something that is broken or incorrect
+labels:
+  - ":bug: bug"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: This is a public repository! Do not reveal any internal information.
+        Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug.
+        In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment if possible.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+      placeholder: |
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```bash
+        pip install session-info
+        ```
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        anndata             0.8.0rc2.dev27+ge524389
+        session_info        1.0.0
+        -----
+        asttokens           NA
+        awkward             1.8.0
+        backcall            0.2.0
+        cython_runtime      NA
+        dateutil            2.8.2
+        debugpy             1.6.0
+        decorator           5.1.1
+        entrypoints         0.4
+        executing           0.8.3
+        h5py                3.7.0
+        ipykernel           6.15.0
+        jedi                0.18.1
+        mpl_toolkits        NA
+        natsort             8.1.0
+        numpy               1.22.4
+        packaging           21.3
+        pandas              1.4.2
+        parso               0.8.3
+        pexpect             4.8.0
+        pickleshare         0.7.5
+        pkg_resources       NA
+        prompt_toolkit      3.0.29
+        psutil              5.9.1
+        ptyprocess          0.7.0
+        pure_eval           0.2.2
+        pydev_ipython       NA
+        pydevconsole        NA
+        pydevd              2.8.0
+        pydevd_file_utils   NA
+        pydevd_plugins      NA
+        pydevd_tracing      NA
+        pygments            2.12.0
+        pytz                2022.1
+        scipy               1.8.1
+        setuptools          62.5.0
+        setuptools_scm      NA
+        six                 1.16.0
+        stack_data          0.3.0
+        tornado             6.1
+        traitlets           5.3.0
+        wcwidth             0.2.5
+        zmq                 23.1.0
+        -----
+        IPython             8.4.0
+        jupyter_client      7.3.4
+        jupyter_core        4.10.0
+        -----
+        Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
+        Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
+        -----
+        Session information updated at 2022-07-07 17:55

lamindb-0.76.8/.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 LaminHub, please report them here.
+    - name: Enterprise support
+      url: https://lamin.ai/contact
+      about: If you have non-technical inquiries, please contact us directly.

lamindb-0.76.8/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Propose a new feature for lamindb
+labels:
+  - ":sparkles: feature"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: This is a public repository! Do not reveal any internal information.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+      placeholder: |
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true

lamindb-0.76.8/.github/ISSUE_TEMPLATE/usage_question.yml

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+name: Usage question
+description: Ask a usage question
+labels:
+  - ":children_crossing: ux"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: This is a public repository! Do not reveal any internal information.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Usage question
+      description: Please ask your question.
+      placeholder: |
+        This is a public repository!
+        Do not reveal any internal information.
+    validations:
+      required: true

lamindb-0.76.8/.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches: [release]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_EVENT_NAME: ${{ github.event_name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - "unit-core"
+          - "unit-storage"
+          - "tutorial"
+          - "guide"
+          - "biology"
+          - "faq"
+          - "storage"
+          - "cli"
+    timeout-minutes: 10
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        if: ${{ matrix.group == 'storage' }}
+        with:
+          python-version: "3.9" # run just one job with a different python version
+      - uses: actions/setup-python@v5
+        if: ${{ matrix.group != 'storage' }}
+        with:
+          python-version: "3.11"
+      - name: cache pre-commit
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ 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: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group
+      - run: nox -s "install_ci(group='${{ 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: "3.10" # use 3.10, 3.8 and 3.11 give issues
+      - run: pip install -U 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: "3.11"
+      - 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-0.76.8/.github/workflows/doc-changes.yml

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+name: doc-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    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-0.76.8/.gitignore

@@ -0,0 +1,220 @@
+# LaminDB
+docsbuild/
+docs/lamin.md
+docs/guide/data-validation.ipynb
+docs/guide/knowledge.ipynb
+docs/guide/bionty.ipynb
+docs/guide/lnschema-core.ipynb
+docs/paradisi05_laminopathic_nuclei.jpg
+bionty_docs/
+lnschema_core_docs/
+_build
+mydata/
+lamin-intro/
+lamin-tutorial/
+mytest/
+rds/
+mydb/
+bfx-output/
+scrnaseq-cellranger/
+scrnaseq-cellranger-schmidt22/
+cellranger_run_001
+docs/test-annotate-flexible/
+__MACOSX/
+docs/lamindb.*
+lamin_sphinx
+docs/conf.py
+*.db
+*.lndb
+*.jpg
+*.zarr/
+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-search2
+test-search3
+test-search4
+test-search5
+default_storage
+default_storage_unit_core
+default_storage_unit_storage
+test.ipynb
+run-tests
+
+# 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-0.76.8/.gitmodules

@@ -0,0 +1,18 @@
+[submodule "lnschema-core"]
+	path = sub/lnschema-core
+	url = https://github.com/laminlabs/lnschema-core.git
+[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-0.76.8/.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - 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
+          )
+  - 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: v0.5.5
+    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
+      - 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
+          )