From 0be7953c5a8c3b247c364330579d2a68ba734afb Mon Sep 17 00:00:00 2001
From: Pete Jemian <prjemian@gmail.com>
Date: Fri, 20 Sep 2024 13:23:00 -0500
Subject: [PATCH] ENV #316

---
 environment.yml | 194 ++++++++++++++++++++++++++----------------------
 1 file changed, 104 insertions(+), 90 deletions(-)

diff --git a/environment.yml b/environment.yml
index f8e0b14f..29abe0f1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,107 +1,121 @@
 name: training_2022
 
-#
+# Provide a run-time suite of software supporting various
+# user activities during and after data collection
 
 # use:
 #   date -Is; conda env create -y -f ./environment.yml date -Is
 
+# Copied & adapted from current ./bluesky/environment*.yml file
+
 channels:
+  # - apsu  # Must be first for compatible epics-base, pyepics, pvapy
   - conda-forge
+
+  # due to licensing Terms & Conditions,  don't use the defaults channel.
   - nodefaults
-  - aps-anl-tag
-  # - nsls2forge
+  # Note this advice: https://stackoverflow.com/questions/67695893/
 
 dependencies:
 
-  # --- Python core packages
-  - python
-  - ipython
-  - jupyter
-  - jupyterlab
-  - notebook
+  # Use conda to install only the basics and whatever pip can't install.
+  # This includes binaries such as Qt and hkl.
+  # Everything else by pip.
+
+# -------------------------------------------------------
+  - python =3.11
   - pip
-  - psutil
-
-  # --- testing and quality assurance
-  - black
-  - coverage
-  - coveralls
-  - flake8
-  - pylint
-  - pytest
-
-  # --- Qt
-  - pyqt=5
-  - qt=5
-
-  # --- general support packages
-  - apischema
-  - aps-dm-api >=5
-  - bitshuffle
-  - blosc
-  - epics-base >=7.0.5
-  - h5netcdf
-  - h5py
-  - hdf5plugin
-  - imagecodecs-lite
-  - ipympl
-  - lxml
-  - mongoquery >=1.3.6
-  - pandas
-  - pint
-  - pyEpics >=3.5.0
-  - pymongo
-  - pysumreg
-  - readline !=8.1.2
-  - scikit-image
-  - xlrd
-
-  # --- Bluesky framework packages
-  - apstools >=1.6.15
-  - area-detector-handlers
-  - bluesky-queueserver
-  - bluesky-queueserver-api
-  - bluesky-widgets
-  - bluesky >=1.8.1
-  - databroker-pack
-  - databroker =1.2
-  - hklpy
-  - ophyd >=1.6.3
-  - pydm
-
-  # --- user-requested packages
-  - nexpy
-  - punx
-  - pvview
-  - pymca
-  - pyRestTable
-  - spec2nexus
-  - xrayutilities
-
-  # # --- packaging and publishing
-  # - conda-build
-  # - sphinx
-  # - sphinxcontrib-napoleon
-  # - twine
-  # - versioneer
-
-  # for tiled install (separately, by pip, as above)
-  - anyio
-  - dask
-  - fastapi
-  - httpx
-  - jinja2
-  - lz4
-  - prometheus_client
-  - pydantic
-  - tifffile
-  - uvicorn
+  - apsu::pvapy
+  - apsu::aps-dm-api >=8   # linux-64  osx-64
+  - hkl   # linux-64
+  - nbconvert-pandoc
+  - pandoc >3
+  - pyqt =5
+  - qt =5
 
   - pip:
-    - ophyd-registry
-    - tiled
 
+    # APS-only
+    # - apsbss  # only works on APS subnet
+
+    # user-requested visualization packages
+    - c2dataviewer  # EPICS PVA images
+    - gemviz  # from tiled
+    - mdaviz  # MDA data files
+    - nexpy  # HDF5 and SPEC data files
+    - pymca  # HDF5 and SPEC data files
+
+    # --- user-requested packages
     - https://github.com/BCDA-APS/adl2pydm/archive/main.zip
-    # --- optional Bluesky framework packages for evaluation
-    # - bluesky-webclient is NOT Python software, don't install it this way
-    #    https://github.com/bluesky/bluesky-webclient
+    - ophyd-registry
+    - punx
+    # - pvmail
+    - pvview
+    - pyRestTable
+    - spec2nexus
+    - xrayutilities
+
+    # --- Python core packages
+    - ipython
+    - jupyter
+    - jupyterlab
+    - notebook
+    - numpy <1.999  # avoid any and all numpy 2.0 releases (includes 2.0.0aNNN)
+    - psutil
+
+    # --- general support packages
+    - apischema
+    - bitshuffle
+    - h5py
+    - hdf5plugin
+    # - httpie
+    - imagecodecs-lite
+    - ipympl
+    - lxml
+    - pandas
+    - pint
+    - pymongo
+    # - pysumreg
+    - scikit-image
+    - xlrd
+
+    # --- Bluesky framework packages
+    - apstools
+    - area-detector-handlers
+    - bluesky >=1.12
+    - bluesky-httpserver
+    - bluesky-kafka
+    - bluesky-live
+    - bluesky-queueserver
+    - bluesky-queueserver-api
+    - bluesky-widgets
+    - databroker <=1.999
+    - databroker-pack
+    - happi
+    - hklpy >=1.1.1
+    - httpx >=0.14  # issue #75
+    - ophyd >=1.9
+    - pydm
+    - tiled[all]
+    # https://github.com/pydata/xarray/issues/6818
+    - xarray !=2022.6.0  # incompatible with numpy=1.20
+
+    # --- testing and quality assurance
+    - black
+    - flake8
+    - pylint
+    - pytest
+    - pytest-notebook
+    - ruff
+
+    # --- packaging and publishing
+    - coverage
+    - myst-parser
+    - nbsphinx
+    - pydata-sphinx-theme
+    - pygithub
+    - sphinx
+    - sphinx-design
+    - sphinx-tabs
+    - sphinxcontrib-napoleon
+    - twine