feature: datashare-python CLI

ICIJ · Dec 23, 2024 · 61804a4 · 61804a4
1 parent 6f1713c
commit 61804a4
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Showing 15 changed files with 62 additions and 27 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -17,6 +17,7 @@ jobs:
           tag: ${{ github.ref_name }}
 
   publish-to-dockerhub:
+    if: false
     needs: [ create-release ]
     runs-on: ubuntu-latest
     steps:
@@ -49,7 +50,7 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 
-  publish-pypi:
+  build:
     runs-on: ubuntu-latest
     permissions:
       id-token: write
@@ -58,16 +59,41 @@ jobs:
       url: https://pypi.org/p/datashare-python
     steps:
       - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install build dependencies
         run: pip install build
-      - name: Publish
-        uses: pypa/[email protected]
+      - name: Build the project
+        run: python -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-pypi:
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/datashare-python
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish to PyPi
+        uses: pypa/gh-action-pypi-publish@release/v1
 
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: false
+  cancel-in-progress: false
diff --git a/docs/assets/clone_template.png b/docs/assets/clone_template.png
diff --git a/docs/get-started/build.md b/docs/get-started/build.md
@@ -22,7 +22,16 @@ $ ./datashare-python build datashare-python
 
 ## Publish to [Docker Hub](https://hub.docker.com/)
 
-You can also fork the template repository and use the CI to build and publish the worker image to [Docker Hub](https://hub.docker.com/).
+You can also clone the template repository:
 
-To publish, make sure to set the `DOCKERHUB_USERNAME` and `DOCKERHUB_TOKEN` ([see documentation](https://docs.docker.com/security/for-developers/access-tokens/))
-and then just create a tag to trigger the build.
+<p align="center">
+    <img alt="clone_template.png" src="../../assets/clone_template.png"/>
+</p>
+
+ and use the CI to build and publish the worker image to [Docker Hub](https://hub.docker.com/).
+
+To publish:
+
+- make sure to set the `DOCKERHUB_USERNAME` and `DOCKERHUB_TOKEN` ([see documentation](https://docs.docker.com/security/for-developers/access-tokens/))
+- remove or comment the `:::yml if: false` line in the `publish-to-dockerhub` job of the `.github/pyblish.yml` workflow
+- then commit, create a tag and push it to trigger the build
diff --git a/docs/get-started/implement/index.md b/docs/get-started/implement/index.md
@@ -5,12 +5,9 @@ The [datashare-python](https://github.com/ICIJ/datashare-python) repository is m
 ## Clone the template repository
 
 Start by cloning the [template repository](https://github.com/ICIJ/datashare-python):
-
-<!-- termynal -->
-```console
-$ git clone [email protected]:ICIJ/datashare-python.git
----> 100%
-```
+<p align="center">
+    <img alt="clone_template.png" src="../../assets/clone_template.png"/>
+</p>
 
 ## Explore the codebase
 

diff --git a/docs/get-started/implement/worker-advanced.md b/docs/get-started/implement/worker-advanced.md
@@ -10,11 +10,9 @@ Make sure you've followed the [basic worker example](worker-basic.md) to underst
 
 Start over and clone the [template repository](https://github.com/ICIJ/datashare-python) once again:
 
-<!-- termynal -->
-```console
-$ git clone [email protected]:ICIJ/datashare-python.git
----> 100%
-```
+<p align="center">
+    <img alt="clone_template.png" src="../../../assets/clone_template.png"/>
+</p>
 
 ## Install extra dependencies
 
@@ -205,11 +203,11 @@ We can then run the tests after starting test services using the `datashare-pyth
 <!-- termynal -->
 ```console
 $ ./datashare-python up -d postgresql redis elasticsearch rabbitmq datashare_web
-$ uv run --frozen pytest datashare_python/tests/tasks/test_vectorize.py
+$ uv run --frozen pytest tests/tasks/test_vectorize.py
 ===== test session starts =====
 collected 3 items
 
-datashare_python/tests/tasks/test_vectorize.py ...                                                                                                                                                                                          [100%]
+tests/tasks/test_vectorize.py ...                                                                                                                                                                                          [100%]
 
 ====== 3 passed in 6.87s ======
 ....
@@ -224,5 +222,5 @@ Rather than copy-pasting the above code blocks, you can replace/update your code
 - [`datashare_python/tasks/vectorize.py`](https://github.com/ICIJ/datashare-python/blob/main/docs/src/vectorize.py)
 - [`datashare_python/tasks/dependencies`](https://github.com/ICIJ/datashare-python/blob/main/docs/src/vector_db_dependencies.py)
 - [`datashare_python/app.py`](https://github.com/ICIJ/datashare-python/blob/main/docs/src/vectorize_app.py)
-- [`datashare_python/tests/tasks/test_vectorize.py](https://github.com/ICIJ/datashare-python/blob/main/docs/src/test_vectorize.py)
+- [`tests/tasks/test_vectorize.py](https://github.com/ICIJ/datashare-python/blob/main/docs/src/test_vectorize.py)
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,10 @@
 name = "datashare-python"
 version = "0.1.0"
 description = "Implement Datashare task in Python"
-authors = [{ name = "Clément Doumouro", email = "[email protected]" }]
+authors = [
+    { name = "Clément Doumouro", email = "[email protected]" },
+    { name = "Clément Doumouro", email = "[email protected]" }
+]
 readme = "README.md"
 requires-python = "~=3.11"
 dependencies = [
@@ -15,12 +18,13 @@ dependencies = [
     "transformers~=4.46.3",
     "pycountry>=24.6.1",
     "sentencepiece>=0.2.0",
-    "termynal~=0.12.2",
     "typer>=0.13.1",
     "alive-progress>=3.2.0",
 ]
-[tool.setuptools]
-py-modules = []
+
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
 
 [tool.uv]
 package = true
@@ -51,7 +55,8 @@ dev = [
     "nest-asyncio>=1.6.0",
 ]
 doc = [
-    "mkdocs-material~=9.5.48"
+    "mkdocs-material~=9.5.48",
+    "termynal~=0.12.2",
 ]
 
 [tool.uv.pip]

diff --git a/datashare_python/tests/__init__.py → tests/__init__.py b/datashare_python/tests/__init__.py → tests/__init__.py
diff --git a/datashare_python/tests/cli/__init__.py → tests/cli/__init__.py b/datashare_python/tests/cli/__init__.py → tests/cli/__init__.py
diff --git a/datashare_python/tests/cli/test_tasks.py → tests/cli/test_tasks.py b/datashare_python/tests/cli/test_tasks.py → tests/cli/test_tasks.py
diff --git a/datashare_python/tests/conftest.py → tests/conftest.py b/datashare_python/tests/conftest.py → tests/conftest.py
diff --git a/...python/tests/tasks/test_translate_docs.py → tests/tasks/test_translate_docs.py b/...python/tests/tasks/test_translate_docs.py → tests/tasks/test_translate_docs.py
diff --git a/datashare_python/tests/test_task_client.py → tests/test_task_client.py b/datashare_python/tests/test_task_client.py → tests/test_task_client.py
diff --git a/datashare_python/tests/test_tasks.py → tests/test_tasks.py b/datashare_python/tests/test_tasks.py → tests/test_tasks.py
diff --git a/datashare_python/tests/test_utils.py → tests/test_utils.py b/datashare_python/tests/test_utils.py → tests/test_utils.py
diff --git a/uv.lock b/uv.lock