2023-3.3 envs

.github/workflows/package.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.10", "3.11"]
       fail-fast: false
     env:
       TZ: America/New_York

configs/config-py310.yml

@@ -1,5 +1,5 @@
 docker_image: "quay.io/condaforge/linux-anvil-cos7-x86_64:latest"
-env_name: "2023-3.2-py310"
+env_name: "2023-3.3-py310"
 conda_env_file: "env-py310.yml"
 conda_binary: "mamba"
 python_version: "3.10"
@@ -19,7 +19,7 @@ zenodo_metadata:
     title: "NSLS-II collection conda environment"
     upload_type: "software"
     description: "NSLS-II collection conda environment"
-    version: 2023-3.2
+    version: 2023-3.3
     creators:
       - name: Rakitin, Max
         affiliation: "Brookhaven National Laboratory"

configs/config-py311.yml

@@ -0,0 +1,27 @@
+docker_image: "quay.io/condaforge/linux-anvil-cos7-x86_64:latest"
+env_name: "2023-3.3-py311"
+conda_env_file: "env-py311.yml"
+conda_binary: "mamba"
+python_version: "3.11"
+pkg_name: ""
+pkg_version: ""
+extra_packages: "mamba"
+channels: "-c conda-forge"
+extra_cmd_before_install: "yum install mesa-libGL -y"
+extra_cmd_after_install: "conda remove perl --force -y"
+docker_upload:
+  - ghcr
+  - dockerhub
+  # - quay
+zenodo_upload: "no"
+zenodo_metadata:
+  metadata:
+    title: "NSLS-II collection conda environment"
+    upload_type: "software"
+    description: "NSLS-II collection conda environment"
+    version: 2023-3.3
+    creators:
+      - name: Rakitin, Max
+        affiliation: "Brookhaven National Laboratory"
+      - name: Bischof, Garrett
+        affiliation: "Brookhaven National Laboratory"

envs/env-py310.yml

@@ -1,4 +1,4 @@
-name: 2023-3.2-py310
+name: 2023-3.3-py310
 channels:
   - conda-forge
 dependencies:
@@ -29,7 +29,7 @@ dependencies:
   - chxtools
   - cmasher
   - conda-pack
-  - csxtools >=0.2
+  - csxtools >=0.2.1
   - dash
   - dash-bootstrap-components
   - dask

envs/env-py311.yml

@@ -0,0 +1,213 @@
+name: 2023-3.3-py311
+channels:
+  - conda-forge
+dependencies:
+  #***************************************************************************#
+  #                                                                           #
+  #            Dependencies from the `nsls2-analysis` metapackage             #
+  #                                                                           #
+  #***************************************************************************#
+  - python >=3.11,<3.12
+  - algotom
+  - amostra <=1.0
+  - ansiwrap
+  - area-detector-handlers >=0.0.9
+  - arvpyf
+  - attrs >=18.0
+  - awkward
+  - black
+  - bluesky ==1.10.0
+  - bluesky-adaptive >=0.3.1
+  - bluesky-kafka >=0.10.0
+  - bluesky-live >=0.0.8
+  - bluesky-queueserver >=0.0.19
+  - bluesky-queueserver-api >=0.0.10
+  - bluesky-widgets >=0.0.15
+  - bokeh
+  - boto3
+  - bottleneck
+  - chxtools
+  - cmasher
+  - conda-pack
+  - csxtools >=0.2.1
+  - dash
+  - dash-bootstrap-components
+  - dask
+  - dask-image
+  - dask-jobqueue
+  - dask-ml
+  - dask-xgboost
+  - databroker >=1.2.5,<2.0.0a
+  - databroker-pack
+  - dictdiffer
+  - discorpy
+  - distributed
+  - doi2bib
+  - dpcmaps
+  # - edrixs  # conflicts caused by the latest numexpr, to resolve later.
+  - eiger-io
+  - event-model >=1.19.2
+  - fabio
+  - ffmpeg >=4.0
+  - flake8
+  - globus-sdk
+  - graphviz
+  - grid-strategy
+  - h5py !=3.4
+  - hdf5-external-filter-plugins-bitshuffle
+  - hdf5-external-filter-plugins-lz4
+  - historydict
+  - hvplot
+  - hxntools >=0.6.1
+  - igor
+  - imageio
+  - inflection
+  - intake <=0.6.4
+  - ipykernel
+  - ipympl >=0.1.1
+  - ipython >=7.20.0
+  - ipywidgets >=7.2.1
+  - isort
+  - ispyb
+  - isstools
+  - jedi
+  - jupyter
+  - jupyterlab
+  - legacy-suitcase
+  - lixtools
+  - lmfit
+  - lxml
+  - matplotlib >=3.6.2
+  - memory_profiler
+  - mendeleev
+  - modestimage
+  - mxtools >=1.0.3
+  - napari >=0.4.17
+  - natsort
+  - netcdf4
+  - nexpy >=0.14.8
+  - nodejs
+  - nsls2-detector-handlers >=0.0.3
+  - nslsii >=0.9.1
+  - numexpr >=2.8.0
+  - numpy >=1.20
+  - nyxtools >=0.0.12
+  - oct2py
+  - opencv
+  - openmpi >=4.1.4
+  - ophyd >=1.8.0
+  # pandas and deps
+  - pandas
+  - openpyxl  # used by pandas .to_excel()
+  - pyarrow  # used by pandas .to_parquet()
+  - pytables  # used by pandas .to_hdf()
+  # end of pandas deps
+  - papermill
+  - pdfstream ==0.5.2  # same as in the 2022-2.0-py37 env, https://zenodo.org/records/6462525/files/2022-2.0-py37.yml
+  - peakutils
+  - periodictable
+  - photutils
+  - pillow
+  - pocl  # needed by pyopencl, used by the `xrt` package
+  - pre-commit
+  - prefect
+  - py-xgboost
+  - py4xs
+  - pycentroids
+  - pyepics >=3.4.2
+  - pyfai
+  - pyfftw
+  - pymatgen >=2023.6.28
+  - pymca
+  - pymcr
+  - pymongo >=3.7
+  - pypdf2
+  - pyqt >=5.15.0
+  - pyqtgraph
+  - pystackreg
+  - python-blosc
+  - python-graphviz
+  - pyxrf >=1.0.24
+  - pyzbar
+  - qt >=5.15.0
+  - redis-py
+  - reportlab
+  - requests
+  # - sasview  # does not work with pyqt>=5.15
+  - scikit-beam >=0.0.24
+  - scikit-learn
+  - scipy >=1.9
+  - seaborn
+  - silx
+  - sixtools
+  - slackclient
+  - smi-analysis
+  - sqlalchemy >=2.0.20
+  - suitcase-csv
+  - suitcase-json-metadata
+  - suitcase-jsonl
+  - suitcase-mongo >=0.4.0
+  - suitcase-msgpack
+  - suitcase-specfile
+  - suitcase-tiff >=0.4.0
+  - suitcase-utils
+  - sympy
+  - toml
+  - tomopy >=1.12.2
+  - tornado
+  - tqdm
+  - tzlocal !=3.0
+  - xlrd
+  - xlwt
+  - xmidas >=0.1.2
+  - xray-vision >=0.1.1
+  - xraylarch >=0.9.66
+  - zbar  # dependency of pyzbar
+  # Simulation packages:
+  - oscars
+  - shadow3 >=23.1.4
+  - srwpy >=4.0.0b1
+  - sirepo-bluesky >=0.6.2
+  - xrt
+  - zict <3.0.0
+  - pip:
+    - mimesis
+    - pyhyperscattering[all]
+  #***************************************************************************#
+  #                                                                           #
+  #            Dependencies from the `nsls2-collection` metapackage           #
+  #                                                                           #
+  #***************************************************************************#
+  - bloptools >=0.3.0
+  - bluesky-darkframes >=0.6.0
+  - caproto
+  - emojis
+  - happi
+  - pexpect
+  # - pydm
+  - pyolog >=4.5.0
+  - pyserial
+  - python-confluent-kafka
+  - pyzenodo3
+  - simple-pid
+  - slack-sdk
+  # Beamline-specific packages
+  - hklpy  # [linux]
+  - hxnfly >=0.0.11
+  - kkcalc
+  - ppmac
+  - pychx >=4.1.2
+  - xpdacq ==1.0.0
+  # Debugging tools:
+  - hunter
+  - logging_tree
+  # Profiling tools:
+  - line_profiler
+  - pyinstrument
+  - pyperformance
+  # ML:
+  - botorch
+  - gpytorch
+  - ortools-python
+  - pytorch
+  - scikit-optimize