Dev

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,64 @@
+name: Bug report
+description: File a bug report
+title: '[BUG]'
+labels: "bug :bug:"
+
+body:
+  - type: markdown
+    id: description
+    attributes:
+      value: |
+          ## Before posting a bug report
+          Search existing GitHub issues to make sure the issue does not already exist.
+
+          # Issue description
+          Description of the issue - include code snippets in the Source code section below and screenshots if relevant.
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behavior
+      description: |
+        What do you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual behavior
+      description: |
+        What actually happens?
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any additional information here that might be necessary to reproduce the issue.
+  - type: textarea
+    id: sourcecode
+    attributes:
+      label: Source code
+      description: Please include a minimal non-working example, or any other code related to the issue.
+      render: shell
+  - type: textarea
+    id: tracebacks
+    attributes:
+      label:  Tracebacks
+      description: Please include the error tracebacks related to the issue here.
+      render: shell
+  - type: textarea
+    id: system
+    attributes:
+      label:  System information
+      description: Please provide informations about you python version and os. The command `python -c "import sys; print(sys.version, sys.platform)"` can be used to get this information. Provide also the output of `pip list` command.
+      render: shell
+    validations:
+      required: true
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Existing GitHub issues
+      options:
+        - label: I have searched existing GitHub issues to make sure the issue does not already exist.
+          required: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,44 @@
+name: Feature request
+description: Suggest a new feature
+labels: "enhancement :sparkles:"
+
+body:
+  - type: markdown
+    id: description
+    attributes:
+      value: |
+          ## Before posting a feature request
+          Search existing GitHub issues to make sure the issue does not already exist.
+
+          # Feature description
+          Description of the feature request - include code snippets and screenshots here if relevant.
+  - type: textarea
+    id: details
+    attributes:
+      label: Feature details
+      description: |
+        What feature would you like to have?
+    validations:
+      required: true
+  - type: textarea
+    id: implementation
+    attributes:
+      label: Implementation
+      description: |
+        Do you have an idea for how this could be implemented? Please include those details here.
+  - type: dropdown
+    id: urgency
+    attributes:
+      label: How important would you say this feature is?
+      options:
+        - "1: Not important. Would be nice to have."
+        - "2: Somewhat important. Needed this quarter."
+        - "3: Very important! Blocking work."
+    validations:
+      required: true
+  - type: textarea
+    id: info
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any additional information here. Include potential alternative solutions, or workarounds, as well as references, if any.

.github/pull_request_template.md

@@ -0,0 +1,22 @@
+# Description
+
+Please provide a brief description of the changes you are making in this pull request.
+
+------------------------------------------------------------------------------------------------------------
+
+# Checklist
+
+Please complete the following checklist when submitting a PR. The PR will not be reviewed until all items are checked.
+
+- [ ] All new features include a unit test.
+      Make sure that the tests passed and the coverage is
+      sufficient by running `python run_pytests.py --tests_folder=tests` or 
+      `pytest tests --cov=src --cov-report=term-missing`.
+
+- [ ] All new functions and code are clearly documented.
+
+- [ ] The code is formatted using Black.
+      You can do this by running `black src tests`.
+
+- [ ] The code is type-checked using Mypy.
+      You can do this by running `mypy src tests`.

.github/workflows/build_dist.yml

@@ -6,6 +6,12 @@ on:
 
 permissions:
   contents: write
+  pull-requests: write
+  actions: write
+  checks: write
+  statuses: write
+  issues: write
+  discussions: write
 
 jobs:
   Build-Dist:
@@ -53,7 +59,7 @@ jobs:
         git config --local user.email "action@github.com"
         git config --local user.name "GitHub Action"
         git add pyproject.toml
-        git commit -m "Updating version of pyproject.toml"
+        git diff-index --quiet HEAD || git commit -m "Updating version of pyproject.toml"
 
     - name: Push the new pyproject.toml
       uses: ad-m/github-push-action@master

.github/workflows/tests.yml

@@ -37,13 +37,11 @@ jobs:
     - name: Test Linting
       run: |
         . ./venv/bin/activate
-        black src --check --diff
-        black tests --check --diff
+        black src tests --check --diff
     - name: Test Typing
       run: |
         . ./venv/bin/activate
-        mypy src
-        mypy tests
+        mypy src tests
     - name: Test Notebooks
       run: |
         . ./venv/bin/activate

Dockerfile

@@ -38,7 +38,6 @@ FROM base_stage AS main_stage
 # Files
 WORKDIR $ROOT_DIR
 COPY --from=build_stage $ROOT_DIR ./
-VOLUME data
 
 # Entrypoint
 ENV PATH="venv/bin:$PATH"

docker_files/build_image_and_run.py

@@ -44,6 +44,12 @@ def get_args_parser():
         default=False,
         help="If set, only runs the container without building the image.",
     )
+    parser.add_argument(
+        "--only_build",
+        action=argparse.BooleanOptionalAction,
+        default=False,
+        help="If set, only build the container without running the image.",
+    )
     return parser
 
 
@@ -73,6 +79,15 @@ def build_images(
     print(f"{cmd = }")
     subprocess.run(cmd, shell=True, check=True)
     print(f"Pruned old images")
+
+    save_images_folder = os.path.join(os.path.dirname(__file__), "..", "data", "dockerfiles")
+    os.makedirs(save_images_folder, exist_ok=True)
+    for image in images:
+        savefile = os.path.abspath(os.path.join(save_images_folder, image.replace(":", "-") + ".tar"))
+        print(f"Saving {image} to {savefile}")
+        save_cmd = f"docker save -o {savefile} {image}"
+        subprocess.run(save_cmd, shell=True, check=True)
+        print(f"{image} saved to {savefile}.")
     return images
 
 def run_container(
@@ -100,6 +115,7 @@ def run_container(
     print(f"Running container {container_name} from image {image_name}:{tag}")
     container_args = [
         "--name", container_name,
+        "--gpus all",
         "--detach",
         f"--volume="
         f"{os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'data'))}"
@@ -116,8 +132,6 @@ def run_container(
 
 def main():
     args = get_args_parser().parse_args()
-    if not args.image_name:
-        args.image_name = os.path.basename(os.path.dirname(os.path.dirname(__file__)))
     print(f"Running with args: {json.dumps(vars(args), indent=4)}")
     if args.only_run:
         images = [f"{args.image_name}:{args.tag}"]
@@ -127,12 +141,20 @@ def main():
             tag=args.tag,
             image_name=args.image_name,
         )
+    if args.only_build:
+        return 0
     for image in images:
+        container_img_part = (
+            image
+            .replace("/", "-")
+            .replace(":", "-")
+            .replace(".", "-")
+        )
         run_container(
             image_name=image,
             tag=args.tag,
             args=json.loads(args.args) if args.args else None,
-            container_name=f"{args.image_name}-{args.mode}",
+            container_name=f"{container_img_part}-{args.mode}",
             run_args=["-e", f"MODE={args.mode}"],
         )
     return 0

pyproject.toml

@@ -96,3 +96,6 @@ module = [
     "pythonbasictools",
 ]
 ignore_missing_imports = true
+
+[tool.black]
+line-length = 120

run_pytests.py

@@ -1,14 +1,12 @@
+import argparse
 import json
 import os
 
 import pytest
-import pythonbasictools as pbt
 from pytest_jsonreport.plugin import JSONReport
-from pytest_cov.plugin import CovPlugin
 
 from tests import configs
 from tests.conftest import RUN_SLOW_ARG_NAME
-import argparse
 
 
 def get_args_parser():

tests/conftest.py

@@ -39,9 +39,7 @@ def pytest_collection_modifyitems(config, items):
         pass
     else:
         # print("Skipping slow tests")
-        skipper = pytest.mark.skip(
-            reason=f"Only run when '--{RUN_SLOW_ARG_NAME}=True' is given"
-        )
+        skipper = pytest.mark.skip(reason=f"Only run when '--{RUN_SLOW_ARG_NAME}=True' is given")
         for item in items:
             if "slow" in item.keywords:
                 item.add_marker(skipper)

tests/test_dummy.py

@@ -26,9 +26,7 @@ def test_dummy(dummy):
 def test_attributes(attr):
     assert hasattr(python_template, attr), f"Module does not have attribute {attr}"
     assert getattr(python_template, attr) is not None, f"Attribute {attr} is None"
-    assert isinstance(
-        getattr(python_template, attr), str
-    ), f"Attribute {attr} is not a string"
+    assert isinstance(getattr(python_template, attr), str), f"Attribute {attr} is not a string"
 
 
 def test_main():
@@ -39,13 +37,7 @@ def test_main():
 def test_get_args_parser():
     parser = get_args_parser()
     assert parser is not None, "get_args_parser returned None"
-    assert isinstance(
-        parser, argparse.ArgumentParser
-    ), "get_args_parser did not return an ArgumentParser instance"
+    assert isinstance(parser, argparse.ArgumentParser), "get_args_parser did not return an ArgumentParser instance"
     # Check if the parser has the expected attributes
-    assert hasattr(
-        parser, "description"
-    ), "ArgumentParser does not have a description attribute"
-    assert (
-        parser.description == "Python Template"
-    ), "ArgumentParser description does not match expected value"
+    assert hasattr(parser, "description"), "ArgumentParser does not have a description attribute"
+    assert parser.description == "Python Template", "ArgumentParser description does not match expected value"