v1.13.8

Release v1.13.8
fgcz · Oct 3, 2024 · 8c74f22 · 8c74f22
2 parents 3e8b913 + ee91713
commit 8c74f22
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diff --git a/.github/workflows/complete_release.yml b/.github/workflows/complete_release.yml
@@ -0,0 +1,48 @@
+name: Complete Release
+on:
+  push:
+    branches: [stable]
+  # TODO remove after testing
+  workflow_dispatch:
+jobs:
+  create_tag:
+    name: Create Tag
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Git Config
+        run: |
+          git config --global user.name "bfabricPy Bot"
+          git config --global user.email "bfabricpy-bot-noreply@fgcz.ethz.ch"
+      - name: Create tag (with Python)
+        run: |
+          set -euxo pipefail
+          # Find the version
+          VERSION=$(python3 -c "import tomllib; from pathlib import Path; print(tomllib.loads(Path('pyproject.toml').read_text())['project']['version'], end='')")
+          # Check if tag exists
+          if git rev-parse $VERSION >/dev/null 2>&1; then
+              echo "Tag $VERSION already exists"
+              exit 1
+          fi
+          # Create tag
+          git tag -a $VERSION -m "Release $VERSION"
+          # Push tag
+          git push origin $VERSION
+  publish_documentation:
+    name: Publish Docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/setup-bfabricpy
+        with:
+          python-version: 3.12
+      - name: Publish documentation
+        run: |
+          set -euxo pipefail
+          git fetch --unshallow origin gh-pages
+          git checkout gh-pages && git pull && git checkout -
+          uv run mkdocs gh-deploy
diff --git a/.github/workflows/run_unit_tests.yml b/.github/workflows/run_unit_tests.yml
@@ -11,12 +11,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: ./.github/actions/setup-bfabricpy
+      - uses: actions/setup-python@v2
         with:
           python-version: 3.9
+      - name: Install nox
+        run: pip install nox uv
       - name: Run unit tests
-        # Note: we use cd to double-check that the installation actually worked
-        run: cd bfabric/tests && pytest ./unit
+        run: nox -s tests
   code_style:
     name: Code Style
     runs-on: ubuntu-latest
@@ -34,7 +35,7 @@ jobs:
       - uses: actions/checkout@v4
       - run: sudo apt-get install -y ripgrep
         name: Install ripgrep
-      - run: rg -n TODO bfabric
+      - run: rg -n TODO .
         name: List TODOs
   license_check:
     name: License Check

diff --git a/bfabric/experimental/app_interface/app_runner/_spec.py b/bfabric/experimental/app_interface/app_runner/_spec.py
diff --git a/bfabric/scripts/bfabric_list_not_existing_storage_directories.py b/bfabric/scripts/bfabric_list_not_existing_storage_directories.py
diff --git a/bfabric/tests/unit/test_response_format_dict.py b/bfabric/tests/unit/test_response_format_dict.py
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -10,6 +10,30 @@ Versioning currently follows `X.Y.Z` where
 
 ## \[Unreleased\]
 
+## \[1.13.8\] - 2024-10-03
+
+This release contains mainly internal changes and ongoing development on the experimental app interface functionality.
+
+### Added
+
+- Entities can be compared and sorted by ID now.
+- Show Python version in version info string.
+- Caching for bfabric_list_not_existing_storage_directories.py.
+- (experimental) add initial code for a resource based application dispatch
+- (experimental) new app_runner cli that integrates all commands into a single interface
+
+### Fixed
+
+- bfabric_read.py is a bit more robust if "name" misses and tabular output is requested.
+
+### Changed
+
+- `bfabric.scripts` has been moved into a namespace package `bfabric_scripts` so we can later split it off.
+- (internal) migrate to src layout
+- (experimental) the former `process` step of the app runner has been split into a `process` and `collect` step where,
+    the collect step is responsible for generating the `output.yml` file that will then be used to register the results.
+- (experimental) app runner apps by default reuse the default resource
+
 ## \[1.13.7\] - 2024-09-17
 
 ### Fixed

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,13 +2,10 @@
 requires = ["setuptools >= 61.0"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.packages.find]
-include = ["bfabric*"]
-
 [project]
 name = "bfabric"
 description = "Python client for the B-Fabric WSDL API"
-version = "1.13.7"
+version = "1.13.8"
 license = { text = "GPL-3.0" }
 authors = [
     {name = "Christian Panse", email = "cp@fgcz.ethz.ch"},
@@ -31,6 +28,8 @@ dependencies = [
     "pydantic",
     "eval_type_backport; python_version < '3.10'",
     "python-dateutil >= 2.9.0",
+    "cyclopts",
+    #"platformdirs >= 4.3",
 ]
 
 [project.optional-dependencies]
@@ -54,31 +53,31 @@ Homepage = "https://github.com/fgcz/bfabricPy"
 Repository = "https://github.com/fgcz/bfabricPy"
 
 [project.scripts]
-"bfabric_flask.py"="bfabric.scripts.bfabric_flask:main"
-#bfabric_feeder_resource_autoQC="bfabric.scripts.bfabric_feeder_resource_autoQC:main"
-"bfabric_list_not_existing_storage_directories.py"="bfabric.scripts.bfabric_list_not_existing_storage_directories:main"
-"bfabric_list_not_available_proteomics_workunits.py"="bfabric.scripts.bfabric_list_not_available_proteomics_workunits:main"
-"bfabric_list_workunit_parameters.py"="bfabric.scripts.bfabric_list_workunit_parameters:main"
-"bfabric_upload_resource.py"="bfabric.scripts.bfabric_upload_resource:main"
-"bfabric_logthis.py"="bfabric.scripts.bfabric_logthis:main"
-"bfabric_setResourceStatus_available.py"="bfabric.scripts.bfabric_setResourceStatus_available:main"
-"bfabric_setExternalJobStatus_done.py"="bfabric.scripts.bfabric_setExternalJobStatus_done:main"
-"bfabric_setWorkunitStatus_available.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_available"
-"bfabric_setWorkunitStatus_processing.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_processing"
-"bfabric_setWorkunitStatus_failed.py"="bfabric.scripts.bfabric_setWorkunitStatus:main_failed"
-"bfabric_delete.py"="bfabric.scripts.bfabric_delete:main"
-"bfabric_read.py"="bfabric.scripts.bfabric_read:main"
-"bfabric_read_samples_of_workunit.py"="bfabric.scripts.bfabric_read_samples_of_workunit:main"
-"bfabric_read_samples_from_dataset.py"="bfabric.scripts.bfabric_read_samples_from_dataset:main"
-"bfabric_save_csv2dataset.py"="bfabric.scripts.bfabric_save_csv2dataset:main"
-"bfabric_save_dataset2csv.py"="bfabric.scripts.bfabric_save_dataset2csv:main"
-"bfabric_save_fasta.py"="bfabric.scripts.bfabric_save_fasta:main"
-"bfabric_save_importresource_sample.py"="bfabric.scripts.bfabric_save_importresource_sample:main"
-"bfabric_save_link_to_workunit.py"="bfabric.scripts.bfabric_save_link_to_workunit:main"
-#bfabric_save_resource="bfabric.scripts.bfabric_save_resource:main"
-"bfabric_save_workunit_attribute.py"="bfabric.scripts.bfabric_save_workunit_attribute:main"
-"bfabric_save_workflowstep.py"="bfabric.scripts.bfabric_save_workflowstep:main"
-"bfabric_slurm_queue_status.py"="bfabric.scripts.bfabric_slurm_queue_status:main"
+"bfabric_flask.py"="bfabric_scripts.bfabric_flask:main"
+#bfabric_feeder_resource_autoQC="bfabric_scripts.bfabric_feeder_resource_autoQC:main"
+"bfabric_list_not_existing_storage_directories.py"="bfabric_scripts.bfabric_list_not_existing_storage_directories:main"
+"bfabric_list_not_available_proteomics_workunits.py"="bfabric_scripts.bfabric_list_not_available_proteomics_workunits:main"
+"bfabric_list_workunit_parameters.py"="bfabric_scripts.bfabric_list_workunit_parameters:main"
+"bfabric_upload_resource.py"="bfabric_scripts.bfabric_upload_resource:main"
+"bfabric_logthis.py"="bfabric_scripts.bfabric_logthis:main"
+"bfabric_setResourceStatus_available.py"="bfabric_scripts.bfabric_setResourceStatus_available:main"
+"bfabric_setExternalJobStatus_done.py"="bfabric_scripts.bfabric_setExternalJobStatus_done:main"
+"bfabric_setWorkunitStatus_available.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_available"
+"bfabric_setWorkunitStatus_processing.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_processing"
+"bfabric_setWorkunitStatus_failed.py"="bfabric_scripts.bfabric_setWorkunitStatus:main_failed"
+"bfabric_delete.py"="bfabric_scripts.bfabric_delete:main"
+"bfabric_read.py"="bfabric_scripts.bfabric_read:main"
+"bfabric_read_samples_of_workunit.py"="bfabric_scripts.bfabric_read_samples_of_workunit:main"
+"bfabric_read_samples_from_dataset.py"="bfabric_scripts.bfabric_read_samples_from_dataset:main"
+"bfabric_save_csv2dataset.py"="bfabric_scripts.bfabric_save_csv2dataset:main"
+"bfabric_save_dataset2csv.py"="bfabric_scripts.bfabric_save_dataset2csv:main"
+"bfabric_save_fasta.py"="bfabric_scripts.bfabric_save_fasta:main"
+"bfabric_save_importresource_sample.py"="bfabric_scripts.bfabric_save_importresource_sample:main"
+"bfabric_save_link_to_workunit.py"="bfabric_scripts.bfabric_save_link_to_workunit:main"
+#bfabric_save_resource="bfabric_scripts.bfabric_save_resource:main"
+"bfabric_save_workunit_attribute.py"="bfabric_scripts.bfabric_save_workunit_attribute:main"
+"bfabric_save_workflowstep.py"="bfabric_scripts.bfabric_save_workflowstep:main"
+"bfabric_slurm_queue_status.py"="bfabric_scripts.bfabric_slurm_queue_status:main"
 
 [tool.black]
 line-length = 120
@@ -99,3 +98,8 @@ using = "PEP631"
 
 [tool.pytest.ini_options]
 logot_capturer = "logot.loguru.LoguruCapturer"
+
+[tool.check-tests-structure]
+sources_path = "src/bfabric"
+tests_path = "tests/unit"
+allow_missing_tests = true
diff --git a/bfabric/__init__.py → src/bfabric/__init__.py b/bfabric/__init__.py → src/bfabric/__init__.py
diff --git a/bfabric/bfabric.py → src/bfabric/bfabric.py b/bfabric/bfabric.py → src/bfabric/bfabric.py
@@ -15,6 +15,7 @@
 
 import base64
 import importlib.metadata
+import sys
 from contextlib import AbstractContextManager
 from contextlib import contextmanager
 from datetime import datetime
@@ -257,8 +258,9 @@ def _get_version_message(self) -> tuple[str, str]:
         engine_name = self._engine.__class__.__name__
         base_url = self.config.base_url
         user_name = f"U={self._auth.login if self._auth else None}"
+        python_version = f"PY={sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}"
         return (
-            f"bfabricPy v{package_version} ({engine_name}, {base_url}, {user_name})",
+            f"bfabricPy v{package_version} ({engine_name}, {base_url}, {user_name}, {python_version})",
             f"Copyright (C) 2014-{year} Functional Genomics Center Zurich",
         )
 

diff --git a/bfabric/bfabric2.py → src/bfabric/bfabric2.py b/bfabric/bfabric2.py → src/bfabric/bfabric2.py
diff --git a/bfabric/bfabric_config.py → src/bfabric/bfabric_config.py b/bfabric/bfabric_config.py → src/bfabric/bfabric_config.py
diff --git a/bfabric/bfabric_legacy.py → src/bfabric/bfabric_legacy.py b/bfabric/bfabric_legacy.py → src/bfabric/bfabric_legacy.py
diff --git a/bfabric/cli_formatting.py → src/bfabric/cli_formatting.py b/bfabric/cli_formatting.py → src/bfabric/cli_formatting.py
diff --git a/bfabric/config/__init__.py → src/bfabric/config/__init__.py b/bfabric/config/__init__.py → src/bfabric/config/__init__.py
diff --git a/bfabric/config/bfabric_auth.py → src/bfabric/config/bfabric_auth.py b/bfabric/config/bfabric_auth.py → src/bfabric/config/bfabric_auth.py
diff --git a/bfabric/config/bfabric_client_config.py → src/bfabric/config/bfabric_client_config.py b/bfabric/config/bfabric_client_config.py → src/bfabric/config/bfabric_client_config.py
diff --git a/bfabric/config/config_file.py → src/bfabric/config/config_file.py b/bfabric/config/config_file.py → src/bfabric/config/config_file.py
diff --git a/bfabric/engine/__init__.py → src/bfabric/engine/__init__.py b/bfabric/engine/__init__.py → src/bfabric/engine/__init__.py
diff --git a/bfabric/engine/engine_suds.py → src/bfabric/engine/engine_suds.py b/bfabric/engine/engine_suds.py → src/bfabric/engine/engine_suds.py
diff --git a/bfabric/engine/engine_zeep.py → src/bfabric/engine/engine_zeep.py b/bfabric/engine/engine_zeep.py → src/bfabric/engine/engine_zeep.py
diff --git a/bfabric/engine/response_format_suds.py → src/bfabric/engine/response_format_suds.py b/bfabric/engine/response_format_suds.py → src/bfabric/engine/response_format_suds.py
diff --git a/bfabric/entities/__init__.py → src/bfabric/entities/__init__.py b/bfabric/entities/__init__.py → src/bfabric/entities/__init__.py
diff --git a/bfabric/entities/application.py → src/bfabric/entities/application.py b/bfabric/entities/application.py → src/bfabric/entities/application.py
diff --git a/bfabric/entities/core/__init__.py → src/bfabric/entities/core/__init__.py b/bfabric/entities/core/__init__.py → src/bfabric/entities/core/__init__.py
diff --git a/bfabric/entities/core/entity.py → src/bfabric/entities/core/entity.py b/bfabric/entities/core/entity.py → src/bfabric/entities/core/entity.py
@@ -67,6 +67,12 @@ def get(self, key: str, default: Any = None) -> Any:
         """Returns the value of a key in the data dictionary, or a default value if the key is not present."""
         return self.__data_dict.get(key, default)
 
+    def __lt__(self, other: Entity) -> bool:
+        """Compares the entity with another entity based on their IDs."""
+        if self.ENDPOINT != other.ENDPOINT:
+            return NotImplemented
+        return self.id < other.id
+
     def __repr__(self) -> str:
         """Returns the string representation of the workunit."""
         return f"{self.__class__.__name__}({repr(self.__data_dict)}, client={repr(self.__client)})"

diff --git a/bfabric/entities/core/has_many.py → src/bfabric/entities/core/has_many.py b/bfabric/entities/core/has_many.py → src/bfabric/entities/core/has_many.py
diff --git a/bfabric/entities/core/has_one.py → src/bfabric/entities/core/has_one.py b/bfabric/entities/core/has_one.py → src/bfabric/entities/core/has_one.py
diff --git a/bfabric/entities/core/relationship.py → src/bfabric/entities/core/relationship.py b/bfabric/entities/core/relationship.py → src/bfabric/entities/core/relationship.py
diff --git a/bfabric/entities/dataset.py → src/bfabric/entities/dataset.py b/bfabric/entities/dataset.py → src/bfabric/entities/dataset.py
diff --git a/bfabric/entities/executable.py → src/bfabric/entities/executable.py b/bfabric/entities/executable.py → src/bfabric/entities/executable.py
diff --git a/bfabric/entities/externaljob.py → src/bfabric/entities/externaljob.py b/bfabric/entities/externaljob.py → src/bfabric/entities/externaljob.py
diff --git a/bfabric/entities/multiplexid.py → src/bfabric/entities/multiplexid.py b/bfabric/entities/multiplexid.py → src/bfabric/entities/multiplexid.py
diff --git a/bfabric/entities/multiplexkit.py → src/bfabric/entities/multiplexkit.py b/bfabric/entities/multiplexkit.py → src/bfabric/entities/multiplexkit.py
diff --git a/bfabric/entities/order.py → src/bfabric/entities/order.py b/bfabric/entities/order.py → src/bfabric/entities/order.py
diff --git a/bfabric/entities/parameter.py → src/bfabric/entities/parameter.py b/bfabric/entities/parameter.py → src/bfabric/entities/parameter.py
diff --git a/bfabric/entities/project.py → src/bfabric/entities/project.py b/bfabric/entities/project.py → src/bfabric/entities/project.py
diff --git a/bfabric/entities/resource.py → src/bfabric/entities/resource.py b/bfabric/entities/resource.py → src/bfabric/entities/resource.py
diff --git a/bfabric/entities/storage.py → src/bfabric/entities/storage.py b/bfabric/entities/storage.py → src/bfabric/entities/storage.py
diff --git a/bfabric/entities/workunit.py → src/bfabric/entities/workunit.py b/bfabric/entities/workunit.py → src/bfabric/entities/workunit.py
diff --git a/bfabric/errors.py → src/bfabric/errors.py b/bfabric/errors.py → src/bfabric/errors.py
diff --git a/.../examples/compare_zeep_suds_pagination.py → .../examples/compare_zeep_suds_pagination.py b/.../examples/compare_zeep_suds_pagination.py → .../examples/compare_zeep_suds_pagination.py
diff --git a/bfabric/examples/compare_zeep_suds_query.py → ...abric/examples/compare_zeep_suds_query.py b/bfabric/examples/compare_zeep_suds_query.py → ...abric/examples/compare_zeep_suds_query.py
diff --git a/bfabric/examples/exists_multi.py → src/bfabric/examples/exists_multi.py b/bfabric/examples/exists_multi.py → src/bfabric/examples/exists_multi.py
diff --git a/bfabric/examples/zeep_debug.py → src/bfabric/examples/zeep_debug.py b/bfabric/examples/zeep_debug.py → src/bfabric/examples/zeep_debug.py
diff --git a/bfabric/experimental/README.md → src/bfabric/experimental/README.md b/bfabric/experimental/README.md → src/bfabric/experimental/README.md
diff --git a/bfabric/experimental/__init__.py → src/bfabric/experimental/__init__.py b/bfabric/experimental/__init__.py → src/bfabric/experimental/__init__.py
diff --git a/...ic/experimental/app_interface/__init__.py → ...ic/experimental/app_interface/__init__.py b/...ic/experimental/app_interface/__init__.py → ...ic/experimental/app_interface/__init__.py
diff --git a/...ntal/app_interface/app_runner/__init__.py → ...ntal/app_interface/app_runner/__init__.py b/...ntal/app_interface/app_runner/__init__.py → ...ntal/app_interface/app_runner/__init__.py
diff --git a/...ntal/app_interface/app_runner/__main__.py → ...ntal/app_interface/app_runner/__main__.py b/...ntal/app_interface/app_runner/__main__.py → ...ntal/app_interface/app_runner/__main__.py