handled CI/CD and .toml files

.gitlab-ci.yml

@@ -11,60 +11,42 @@ include:
    file: acc_py_devtools/templates/gitlab-ci/python.yml
 
 variables:
-  project_name: caimira
+  PY_VERSION: "3.11"
 
 
 # ###################################################################################################
 # Test code - CAiMIRA (model) and CERN CAiMIRA (CERN's UI)
 
-  # A full installation of CAiMIRA, tested with pytest.
-test_install:
-  extends: .acc_py_full_test
-  variables:
-    project_root: ./caimira
-    project_name: caimira
+.py_full_test:
+  image: registry.cern.ch/docker.io/library/python:${PY_VERSION}
+  stage: test
+  before_script:
+    - pip install -e ${caimira_root}[test]
+    - pip install -e ${cern_caimira_root}[test]
+  script:
+    - cd ${caimira_root}
+    - python -m pytest
+    - cd ../${cern_caimira_root}
+    - python -m pytest
 
 
-# A development installation of CAiMIRA tested with pytest.
-test_dev:
-  extends: .acc_py_dev_test
+# A full installation of CAiMIRA, tested with pytest.
+caimira_full_test:
+  extends: .py_full_test
   variables:
-    project_root: ./caimira
-    project_name: caimira
+    caimira_root: ./caimira
+    cern_caimira_root: ./cern_caimira 
 
 
 # A development installation of CAiMIRA tested with pytest.
-test_dev-39:
+caimira_full_test-39:
+  extends: .py_full_test
   variables:
     PY_VERSION: "3.9"
-    project_root: ./caimira
-    project_name: caimira
-  extends: .acc_py_dev_test
-
-# A full installation of CERN CAiMIRA, tested with pytest.
-test_install_cern_caimira:
-  extends: .acc_py_full_test
-  variables:
-    project_root: ./_cern_caimira
-    project_name: cern_caimira
+    caimira_root: ./caimira
+    cern_caimira_root: ./cern_caimira 
 
 
-# A development installation of CERN CAiMIRA tested with pytest.
-test_dev_cern_caimira:
-  extends: .acc_py_dev_test
-  variables:
-    project_root: ./_cern_caimira
-    project_name: cern_caimira
-
-
-# A development installation of CERN CAiMIRA tested with pytest.
-test_dev-39_cern_caimira:
-  variables:
-    PY_VERSION: "3.9"
-    project_root: ./_cern_caimira
-    project_name: cern_caimira
-  extends: .acc_py_dev_test
-
 # ###################################################################################################
 # Test OpenShift config
 

caimira/pyproject.toml

@@ -18,27 +18,21 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "ipykernel",
-    "ipympl>=0.9.0",
-    "ipywidgets<8.0",
-    "Jinja2",
-    "loky",
     "matplotlib",
     "memoization",
     "mistune",
     "numpy",
     "pandas",
-    "psutil",
     "pyinstrument",
-    "pyjwt",
     "python-dateutil",
+    "requests",
     "retry",
     "ruptures",
     "scipy",
     "scikit-learn",
+    "tabulate",
     "timezonefinder",
     "tornado",
-    "types-retry",
 ]
 
 [project.optional-dependencies]
@@ -51,7 +45,8 @@ test = [
     "numpy-stubs @ git+https://github.com/numpy/numpy-stubs.git",
     "types-dataclasses",
     "types-python-dateutil",
-    "types-requests"
+    "types-requests",
+    "types-retry",
 ]
 doc = [
     "sphinx",
@@ -71,40 +66,7 @@ addopts = "--mypy"
 [tool.mypy]
 no_warn_no_return = true
 exclude = "caimira/profiler.py"
-ignore_missing_imports = true # TODO what to do here? 
-
-[tool.mypy-loky]
-ignore_missing_imports = true
-
-[tool.mypy-ipympl]
-ignore_missing_imports = true
-
-[tool.mypy-ipywidgets]
-ignore_missing_imports = true
-
-[tool.mypy-matplotlib]
-ignore_missing_imports = true
-
-[tool.mypy-mistune]
-ignore_missing_imports = true
-
-[tool.mypy-qrcode]
-ignore_missing_imports = true
-
-[tool.mypy-scipy]
-ignore_missing_imports = true
-
-[tool.mypy-timezonefinder]
-ignore_missing_imports = true
-
-[tool.mypy-pandas]
-ignore_missing_imports = true
-
-[tool.mypy-pstats]
-follow_imports = "skip"
-
-[tool.mypy-tabulate]
-ignore_missing_imports = true
 
-[tool.mypy-ruptures]
+[[tool.mypy.overrides]]
+module = ["pandas", "ruptures", "scipy.*", "setuptools", "sklearn.*", "tabulate"]
 ignore_missing_imports = true

caimira/src/caimira/calculator/models/monte_carlo/sampleable.py

@@ -1,7 +1,7 @@
 import typing
 
 import numpy as np
-from sklearn.neighbors import KernelDensity # type: ignore
+from sklearn.neighbors import KernelDensity
 
 from caimira.calculator.models import models
 

caimira/src/caimira/scripts/data/vaccine_effectiveness.py

@@ -1,5 +1,5 @@
-# import pandas as pd
-# from tabulate import tabulate
+import pandas as pd
+from tabulate import tabulate
 
 '''
 Script file to generate the vaccine effectiveness values.

cern_caimira/pyproject.toml

@@ -70,7 +70,11 @@ addopts = "--mypy"
 
 [tool.mypy]
 no_warn_no_return = true
-ignore_missing_imports = true # TODO what to do here? 
+
+[[tool.mypy.overrides]]
+module = ["caimira.*", "ipympl.*", "loky", "ipywidgets", "setuptools", "pandas"]
+ignore_missing_imports = true
+
 
 [tool.mypy-loky]
 ignore_missing_imports = true