Chore/upgrade dependencies (#188)

* docs: clarify styling comment Signed-off-by: F.N. Claessen <[email protected]> * feat: `make test` tests optional parts, too Signed-off-by: F.N. Claessen <[email protected]> * chore: add classifiers for Python 3.10 and 3.11 Signed-off-by: F.N. Claessen <[email protected]> * chore: move requirements to python-version-specific folder Signed-off-by: F.N. Claessen <[email protected]> * feature: make command to upgrade deps Signed-off-by: F.N. Claessen <[email protected]> * chore: missing commands from listing, and define commands in the same order as the listing Signed-off-by: F.N. Claessen <[email protected]> * feature: add requirements.txt for Python 3.11 Signed-off-by: F.N. Claessen <[email protected]> * chore: update dev docs Signed-off-by: F.N. Claessen <[email protected]> * refactor: `make test` uses all tests straightaway Signed-off-by: F.N. Claessen <[email protected]> * feature: ensure dependencies folder Signed-off-by: F.N. Claessen <[email protected]> * fix: installation dependencies for all tests Signed-off-by: F.N. Claessen <[email protected]> * docs: obsolete comment Signed-off-by: F.N. Claessen <[email protected]> * feature: allow skipping test when upgrading dependencies Signed-off-by: F.N. Claessen <[email protected]> * refactor: move test dependencies to `make install-for-test` Signed-off-by: F.N. Claessen <[email protected]> * feature: test the core with fewer pinned dependencies, and then test everything with share dependencies Signed-off-by: F.N. Claessen <[email protected]> * chore: unpin numpy and scipy in optional forecast dependencies Signed-off-by: F.N. Claessen <[email protected]> * chore: unpin pandas for 3.11 and higher Signed-off-by: F.N. Claessen <[email protected]> * feature: automate test pipeline for Python 3.11 Signed-off-by: F.N. Claessen <[email protected]> * fix: AttributeError: `np.NaN` was removed in the NumPy 2.0 release. Use `np.nan` instead. Signed-off-by: F.N. Claessen <[email protected]> * Revert "chore: unpin pandas for 3.11 and higher" This reverts commit c574364. * feature: automate test pipeline for Python 3.12 (#190) Signed-off-by: F.N. Claessen <[email protected]> * fix(deps): pin only from 3.11 onwards Signed-off-by: F.N. Claessen <[email protected]> * Revert "fix(deps): pin only from 3.11 onwards" This reverts commit e9ffb4d. --------- Signed-off-by: F.N. Claessen <[email protected]>
SeitaBV · Sep 20, 2024 · 62e1a76 · 62e1a76
1 parent f0b9053
commit 62e1a76
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diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        py_version: [ '3.7', '3.8', '3.9', '3.10' ]
+        py_version: [ '3.7', '3.8', '3.9', '3.10', '3.11', '3.12' ]
         include:
           - py_version: '3.7'
             skip-viz: true

diff --git a/Makefile b/Makefile
@@ -1,33 +1,61 @@
-# Note: use tabs
+# Check Python major and minor version
+# For more information, see https://stackoverflow.com/a/22105036
+PYV = $(shell python -c "import sys;t='{v[0]}.{v[1]}'.format(v=list(sys.version_info[:2]));sys.stdout.write(t)")
+
+# Note: use tabs (not spaces) for indentation
 # actions which are virtual, i.e. not a script
-.PHONY: install-deps install-tb freeze-deps test
+.PHONY: install install-deps install-tb install-for-test freeze-deps upgrade-deps test test-core test-forecast test-viz ensure-deps-folder
 
 install: install-deps install-tb
 
+install-for-test:
+	pip install setuptools_scm pytest
+
 install-deps:
 	pip install --upgrade pip-tools
-	pip-sync dev/requirements.txt
+	pip-sync dev/${PYV}/requirements.txt
 	pip install pre-commit
 
-freeze-deps:
-	pip install --upgrade pip-tools
-	pip-compile -o dev/requirements.txt	 # use --upgrade or --upgrade-package to actually change versions
-
 install-tb:
 	pip install -e .
 	pre-commit install
 
+freeze-deps:
+	make ensure-deps-folder
+	pip install --upgrade pip-tools
+	pip-compile -o dev/${PYV}/requirements.txt
+
+upgrade-deps:
+	make ensure-deps-folder
+	pip install --upgrade pip-tools
+	pip-compile -o dev/${PYV}/requirements.txt --upgrade
+ifneq ($(skip-test), yes)
+	make test
+endif
+
 test:
+	make test-core  # test just the core, which may have fewer pinned dependencies
+	make test-all  # test everything sharing the same dependencies
+
+test-all:
+	pip install -e .[forecast,viz]
+	make install-for-test
+	pytest
+
+test-core:
 	pip install -e .
-	pip install setuptools_scm pytest
+	make install-for-test
 	pytest --ignore test_forecast__ --ignore test_viz__
 
 test-forecast:
 	pip install -e .[forecast]
-	pip install setuptools_scm pytest
+	make install-for-test
 	pytest -k test_forecast__
 
 test-viz:
 	pip install -e .[viz]
-	pip install setuptools_scm pytest
+	make install-for-test
 	pytest -k test_viz__
+
+ensure-deps-folder:
+	mkdir -p dev/${PYV}
diff --git a/dev/3.11/requirements.txt b/dev/3.11/requirements.txt
@@ -0,0 +1,52 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --output-file=dev/3.11/requirements.txt
+#
+dill==0.3.8
+    # via openturns
+greenlet==3.1.0
+    # via sqlalchemy
+importlib-metadata==8.5.0
+    # via timely-beliefs (setup.py)
+isodate==0.6.1
+    # via timely-beliefs (setup.py)
+numpy==1.26.4 ; python_version > "3.7"
+    # via
+    #   pandas
+    #   properscoring
+    #   scipy
+    #   timely-beliefs (setup.py)
+openturns==1.23
+    # via timely-beliefs (setup.py)
+pandas==2.2.1 ; python_version > "3.7"
+    # via timely-beliefs (setup.py)
+properscoring==0.1
+    # via timely-beliefs (setup.py)
+psutil==6.0.0
+    # via openturns
+psycopg2-binary==2.9.9
+    # via timely-beliefs (setup.py)
+python-dateutil==2.9.0.post0
+    # via pandas
+pytz==2024.2
+    # via
+    #   pandas
+    #   timely-beliefs (setup.py)
+scipy==1.14.1 ; python_version > "3.7"
+    # via
+    #   properscoring
+    #   timely-beliefs (setup.py)
+six==1.16.0
+    # via
+    #   isodate
+    #   python-dateutil
+sqlalchemy==2.0.35
+    # via timely-beliefs (setup.py)
+typing-extensions==4.12.2
+    # via sqlalchemy
+tzdata==2024.1
+    # via pandas
+zipp==3.20.2
+    # via importlib-metadata
diff --git a/dev/requirements.txt → dev/3.9/requirements.txt b/dev/requirements.txt → dev/3.9/requirements.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile --output-file=dev/requirements.txt
+#    pip-compile --output-file=dev/3.9/requirements.txt
 #
 altair==4.1.0
     # via timely-beliefs (setup.py)

diff --git a/dev/dev.md b/dev/dev.md
@@ -21,8 +21,8 @@ And run tests:
 
 To update dependencies run:
 
-    pip-compile -o dev/requirements.txt -U
+    make upgrade-deps
 
 To install dependencies run:
 
-    pip install -r dev/requirements.txt
+    make install-deps
diff --git a/pyproject.toml b/pyproject.toml
@@ -22,6 +22,8 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: MIT License",
@@ -65,8 +67,7 @@ viz = [
 ]
 forecast = [
     "sktime",
-    "numpy<1.25,>=1.21.0; python_version > '3.7'",  # required by sktime==0.15.0
-    "scipy<2.0.0; python_version > '3.7'",  # required by sktime==0.15.0
+    "numpy>=1.21.0; python_version > '3.7'",  # required by sktime==0.15.0
 ]
 
 [project.readme]

diff --git a/timely_beliefs/tests/test_df_resampling.py b/timely_beliefs/tests/test_df_resampling.py
@@ -303,7 +303,7 @@ def test_downsample_once_upsample_once_around_dst(
     df = df_wxyz(
         time_slot_sensor, 25, 1, 1, 1, start
     )  # 1 deterministic belief per event
-    df.iloc[0] = np.NaN  # introduce 1 NaN value
+    df.iloc[0] = np.nan  # introduce 1 NaN value
     print(df)
 
     # Downsample the original frame