lamindb 0.74.3__tar.gz → 0.75.1__tar.gz

{lamindb-0.74.3 → lamindb-0.75.1}/.github/workflows/build.yml

@@ -63,7 +63,7 @@ jobs:
         run: sudo apt-get -y install graphviz
       - run: nox -s lint
         if: ${{ matrix.group == 'tutorial' }} # choose a fast-running a group
-      - run: nox -s "install(group='${{ matrix.group }}')"
+      - run: nox -s "install_ci(group='${{ matrix.group }}')"
       - uses: aws-actions/configure-aws-credentials@v1
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
@@ -106,7 +106,7 @@ jobs:
         with:
           python-version: "3.10" # use 3.10, 3.8 and 3.11 give issues
       - run: pip install -U laminci
-      - run: nox -s "install(group='docs')"
+      - run: nox -s "install_ci(group='docs')"
       - uses: actions/download-artifact@v2
       - run: nox -s docs
       - uses: nwtgck/actions-netlify@v1.2

{lamindb-0.74.3 → lamindb-0.75.1}/.gitmodules

@@ -4,9 +4,6 @@
 [submodule "sub/lamindb-setup"]
 	path = sub/lamindb-setup
 	url = https://github.com/laminlabs/lamindb-setup
-[submodule "sub/lnschema-bionty"]
-	path = sub/lnschema-bionty
-	url = https://github.com/laminlabs/lnschema-bionty
 [submodule "sub/lamin-cli"]
 	path = sub/lamin-cli
 	url = https://github.com/laminlabs/lamin-cli

{lamindb-0.74.3/sub/lnschema-bionty → lamindb-0.75.1}/.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
               docs/notes/
           )
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.5.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -48,8 +48,7 @@ repos:
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]
-        additional_dependencies:
-          ["types-pkg-resources", "types-requests", "types-attrs"]
+        additional_dependencies: ["types-requests", "types-attrs"]
         exclude: |
           (?x)(
               test_notebooks.py

lamindb-0.75.1/CONTRIBUTING.md

@@ -0,0 +1,94 @@
+# Contributing
+
+Contributions are generally welcome. Please make an issue to discuss proposals.
+
+## Installation
+
+### PyPI
+
+For installation from PyPI, see [docs.lamin.ai/setup](https://docs.lamin.ai/setup).
+
+### Github
+
+For installation from GitHub, call:
+
+```bash
+git clone --recursive https://github.com/laminlabs/lamindb
+pip install laminci
+nox -s install
+```
+
+This will install a few dependencies from the git submodules linked [here](https://github.com/laminlabs/lamindb/tree/main/sub).
+lamindb depends on several other packages that may require modifications for pull requests to successfully pass the continuous integration build.
+We suggest the following workflow if commits to any of the submodules are essential for the current modifications in lamindb:
+
+1. Change directory into the submodule that you want to modify: `cd sub/SUBMODULE`.
+2. Switch to a new feature branch: `git switch -c feature/NEWFEATURE`.
+3. Make a pull request with your changes to the `SUBMODULE` and ensure that the CI passes.
+4. In the repository root of lamindb, create a new commit and push:
+
+```bash
+cd ..
+git add -u
+git commit -m "Upgraded SUBMODULE"
+git push
+```
+
+Any pull request of yours should now also have the changes of the submodule included allowing you to test that changes in the submodule and lamindb are compatible.
+
+## Running and writing tests
+
+This package uses the [pytest][] for automated testing.
+Please add a test for every function added to the package.
+
+Running tests requires the [Docker daemon][] up, then run at the root of the repository:
+
+```bash
+pytest
+```
+
+in the root of the repository.
+Continuous integration will automatically run the tests on all pull requests.
+
+## Code-style
+
+This project uses [pre-commit][] to enforce consistent code-styles. On every commit, pre-commit checks will either
+automatically fix issues with the code, or raise an error message.
+
+To enable pre-commit locally, simply run
+
+```bash
+pre-commit install
+```
+
+in the root of the repository. Pre-commit will automatically download all dependencies when it is run for the first time.
+
+We further use [gitmoji][] to add emoticons to commits.
+These allow us to more easily categorize them allowing for faster visual filtering.
+
+It can be installed by running:
+
+```bash
+npm i -g gitmoji-cli
+```
+
+and enabled for the repository via:
+
+```bash
+gitmoji -i
+```
+
+## Documentation
+
+We build our documentation with an internal tool called `lndocs`.
+We have not made it public yet and therefore external contributors need to rely on the Github Actions `docs` job to build the documentation.
+If the `docs` job succeeds, a preview URL will be posted automatically as a comment to your pull request.
+
+## Releases
+
+Currently only lamin employees have release rights.
+
+[Docker daemon]: https://docs.docker.com/engine/install/
+[gitmoji]: https://gitmoji.dev/
+[pre-commit]: https://pre-commit.com/
+[pytest]: https://docs.pytest.org/

{lamindb-0.74.3 → lamindb-0.75.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.3
+Version: 0.75.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.70.5
-Requires-Dist: lamindb_setup==0.74.2
+Requires-Dist: lnschema_core==0.72.2
+Requires-Dist: lamindb_setup==0.76.3
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.15.0
+Requires-Dist: lamin_cli==0.16.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.3 ; extra == "bionty"
+Requires-Dist: bionty==0.48.0 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"

{lamindb-0.74.3 → lamindb-0.75.1}/docs/api.md

@@ -20,7 +20,7 @@ lamindb
 
 ```{toctree}
 :maxdepth: 1
-:caption: Plug-ins
+:caption: Plugins
 :hidden:
 
 bionty
@@ -32,6 +32,5 @@ wetlab
 :caption: Utilities
 :hidden:
 
-bionty-base
 readfcs
 ```