Merge pull request #341 from ZLLentz/rel-5.9.0

ENH: pcds-5.9.0

.github/workflows/integration_test.yaml

@@ -26,13 +26,14 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: mamba env create -q -n pcds-test -f envs/pcds/env.yaml
     - uses: ./.github/actions/finalize_and_check_env
     - uses: ./.github/actions/run_tests
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
   # The env from current-env-tests + the latest tags slapped onto it
   py39-next-incr:
     defaults:
@@ -45,6 +46,7 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: |
         cd scripts
         python update_tags.py pcds
@@ -54,15 +56,18 @@ jobs:
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
     - name: Environment Export
-      if: always()
-      run: conda env export --file export.yaml
+      id: export
+      if: steps.create.outcome == 'success'
+      run: |
+        conda activate base
+        python scripts/export_env.py --rel test --base pcds
     - uses: actions/upload-artifact@v4
-      if: always()
+      if: steps.export.outcome == 'success'
       with:
         name: incr_env.yaml
-        path: "export.yaml"
+        path: "envs/pcds/env.yaml"
   # Start from scratch to get some py39 testing done
   # This is a fallback alternative to py39-next-incr, which is preferred
   py39-next-full:
@@ -76,6 +81,7 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: |
         cd scripts
         python update_tags.py pcds
@@ -85,15 +91,18 @@ jobs:
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
     - name: Environment Export
-      if: always()
-      run: conda env export --file export.yaml
+      id: export
+      if: steps.create.outcome == 'success'
+      run: |
+        conda activate base
+        python scripts/export_env.py --rel test --base pcds
     - uses: actions/upload-artifact@v4
-      if: always()
+      if: steps.export.outcome == 'success'
       with:
-        name: next_env.yaml
-        path: "export.yaml"
+        name: py39_env.yaml
+        path: "envs/pcds/env.yaml"
   # Try to build a python 3.10 env
   py310-next-full:
     defaults:
@@ -106,6 +115,7 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: |
         cd scripts
         python update_tags.py pcds
@@ -115,7 +125,18 @@ jobs:
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
+    - name: Environment Export
+      id: export
+      if: steps.create.outcome == 'success'
+      run: |
+        conda activate base
+        python scripts/export_env.py --rel test --base pcds
+    - uses: actions/upload-artifact@v4
+      if: steps.export.outcome == 'success'
+      with:
+        name: py310_env.yaml
+        path: "envs/pcds/env.yaml"
   # Try to build a python 3.11 env
   py311-next-full:
     defaults:
@@ -128,6 +149,7 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: |
         cd scripts
         python update_tags.py pcds
@@ -137,7 +159,18 @@ jobs:
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
+    - name: Environment Export
+      id: export
+      if: steps.create.outcome == 'success'
+      run: |
+        conda activate base
+        python scripts/export_env.py --rel test --base pcds
+    - uses: actions/upload-artifact@v4
+      if: steps.export.outcome == 'success'
+      with:
+        name: py311_env.yaml
+        path: "envs/pcds/env.yaml"
   py312-next-full:
     defaults:
       run:
@@ -149,6 +182,7 @@ jobs:
         fetch-depth: 0
     - uses: ./.github/actions/conda_setup
     - name: create environment
+      id: create
       run: |
         cd scripts
         python update_tags.py pcds
@@ -158,7 +192,18 @@ jobs:
       with:
         use-tag: true
     - uses: ./.github/actions/release_notes
-      if: always()
+      if: steps.create.outcome == 'success'
+    - name: Environment Export
+      id: export
+      if: steps.create.outcome == 'success'
+      run: |
+        conda activate base
+        python scripts/export_env.py --rel test --base pcds
+    - uses: actions/upload-artifact@v4
+      if: steps.export.outcome == 'success'
+      with:
+        name: py312_env.yaml
+        path: "envs/pcds/env.yaml"
   # Checks which packages are not ready yet for py310
   py310-readiness:
     needs: py310-next-full
@@ -170,10 +215,17 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: ./.github/actions/conda_setup
-    - name: check packages
+    - name: check packages conda
       run: |
         cd scripts
         ./check_py_compat.sh pcds 3.10 | tee ~/compat.log
+    - name: check packages pip
+      if: always()
+      run: |
+        conda create --name test python=3.10
+        conda activate test
+        cd scripts
+        ./check_py_compat_pypi.sh pcds | tee -a ~/compat.log
     - name: summarize failure
       if: failure()
       run:  grep "uninstallable package" ~/compat.log >> "$GITHUB_STEP_SUMMARY"
@@ -188,10 +240,17 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: ./.github/actions/conda_setup
-    - name: check packages
+    - name: check packages conda
       run: |
         cd scripts
         ./check_py_compat.sh pcds 3.11 | tee ~/compat.log
+    - name: check packages pip
+      if: always()
+      run: |
+        conda create --name test python=3.11
+        conda activate test
+        cd scripts
+        ./check_py_compat_pypi.sh pcds | tee -a ~/compat.log
     - name: summarize failure
       if: failure()
       run:  grep "uninstallable package" ~/compat.log >> "$GITHUB_STEP_SUMMARY"
@@ -205,10 +264,17 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: ./.github/actions/conda_setup
-    - name: check packages
+    - name: check packages conda
       run: |
         cd scripts
         ./check_py_compat.sh pcds 3.12 | tee ~/compat.log
+    - name: check packages pip
+      if: always()
+      run: |
+        conda create --name test python=3.12
+        conda activate test
+        cd scripts
+        ./check_py_compat_pypi.sh pcds | tee -a ~/compat.log
     - name: summarize failure
       if: failure()
       run:  grep "uninstallable package" ~/compat.log >> "$GITHUB_STEP_SUMMARY"

envs/pcds/conda-packages.txt

@@ -3,20 +3,20 @@ ads-async>=0.3.1
 anaconda-client>=1.12.3
 apischema>=0.18.0
 archapp>=1.1.0
-atef>=1.4.0
+atef>=1.5.0
 atlassian-python-api>=3.41.14
 black>=24.8.0
 blark>=0.8.1
 bluesky-live>=0.0.8
-bluesky-queueserver>=0.0.18
 bluesky-widgets>=0.0.14
 bokeh>=1.0.1
 botorch>=0.4.0
 caproto>=1.1.1
 coloredlogs>=15.0.1
 conda-pack>=0.8.0
-conda-smithy>=3.38.0
+conda-smithy>=3.39.0
 cookiecutter>=2.1.1
+coverage>=7.6.1
 cython>=0.29.34
 datashader>=0.14.4
 elog>=1.2.3
@@ -25,51 +25,51 @@ flake8>=7.1.1
 flask>=3.0.3
 fzf>=0.54.3
 gdb>=15.1
-gh>=2.54.0
+gh>=2.55.0
+ghapi>=1.0.5
 gpytorch>=1.4.2
-grpcio-tools>=1.51.1
 h5py>=3.3.0
 happi>=2.5.0
 hklpy>=1.1.1
 holoviews>=1.10.9
-hutch-python>=1.20.0
+hutch-python>=1.21.0
 hxrsnd>=0.3.1
 isort>=5.13.2
 jupyter>=1.0.0
 krtc>=0.3.0
 lightpath>=1.0.4
 line_profiler>=4.1.1
-lucid>=0.10.3
+lucid>=0.11.0
 lxml>=4.8.0
 memray>=1.13.4
 mysqlclient>=2.0.3
-nabs>=1.5.4
+nabs>=1.5.5
 numpy>=1.14,<2.0.0
-opencv>=4.5.1
+opencv>=4.5.1[build='^qt5.*$']
 openssl>=3.3.1
 pandas>=1.5.3
 panel>=0.14.4
 papermill>=2.3.4
 paramiko>=3.1.0
 pcaspy>=0.7.3
-pcdscalc>=0.5.1
-pcdsdaq>=2.4.3
-pcdsdevices>=8.4.0
+pcdscalc>=0.6.0
+pcdsdaq>=2.4.4
+pcdsdevices>=8.5.0
 pcdsutils>=0.14.1
 pcdswidgets>=0.8.3
 periodictable>=1.5.2
 pipdeptree>=2.23.1
 pmgr>=2.1.3
 pmpsdb_client>=1.2.0
 pre-commit>=3.8.0
-psdaq-control-minimal>=3.3.38
-psdm_qs_cli>=0.3.7
-pswalker>=1.0.8
+psdaq-control-minimal>=4.1.2
+psdm_qs_cli>=0.3.8
+pswalker>=1.0.10
 pyaudio>=0.2.13
 pyca>=3.2.1
 pycln>=2.4.0
 pydm>=1.24.1
-pyepics>=3.5.6
+pyepics>=3.5.7
 pyfiglet>=0.8
 pymongo>=4.3.3
 py-spy>=0.3.14
@@ -90,8 +90,11 @@ scikit-image>=0.19.3
 scikit-learn>=1.2.2
 scipy>=1.10.1
 seaborn>=0.12.2
+shapely
 shellcheck>=0.10.0
 simplejson>=3.19.1
+sphinx>=7
+sphinx_rtd_theme>=2.0.0
 spyder-kernels>=2.4.3
 suitcase-csv>=0.3.0
 suitcase-json-metadata>=0.2.1
@@ -102,8 +105,8 @@ suitcase-specfile>=0.2.5
 suitcase-tiff>=0.4.0
 timechart>=1.5.3
 toml>=0.10.2
-transfocate>=0.5.8
-typhos>=3.1.1
+transfocate>=0.5.9
+typhos>=4.0.0
 whatrecord>=0.6.0
 xarray>=2023.3.0
 xraylib>=4.1.3
@@ -114,19 +117,16 @@ pyqt=5.15.9
 pyqtwebengine=5.15.9
 # conda+pip regressive pins
 # avoids bluesky v1.11.0 which breaks nabs
-bluesky=1.10.0
-# coverage 7.4.2 does not have a py39 build on conda
-coverage=7.4.1
-# avoids pre-releases of v2
-databroker<2.0.0
+bluesky-base=1.10.0
+# non-tiled databroker required in conda-packages if any package has databroker as a dep
+databroker=1.2.5
 # ipython changes make scientists upset and can break experiments
 ipython=8.4.0
+# matplotlib conda pin can be removed once all conda dependencies specify matplotlib-base
+matplotlib=3.8.4
+# most of the ecosystem is not ready for numpy 2.0
+numpy=1.26.4
 # avoids ophyd v1.8.0 which I have not had time to test
 ophyd=1.7.0
-# force a newer perl build (temporary pin, can remove later if you read this line)
-perl=5.32.1=7_hd590300_perl5
 # pin for gui interface stability
 qtpy=2.1.0
-# sphinx 7.0.0 incompatible with rtd theme at 1.2.0, temporarily pin both
-sphinx<7
-sphinx_rtd_theme=1.2.0