more environments and explicit versions for reproducibility

This commit is contained in:
Steppke Alexander
2022-03-30 23:16:28 +02:00
parent 08effb0224
commit cf94ee142b
4 changed files with 501 additions and 0 deletions

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analysis.yml Normal file
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channels:
- defaults
- paulscherrerinstitute
- conda-forge
dependencies:
- python
- pip
# numpy pinned until numba is compatible with newer versions
- numpy==1.21.5
- scipy
- pandas
- numba
- matplotlib
- ipython
- jupyterlab
- ipympl
- joblib
- black
- pytest
- h5py
# Jupyterlab extensions
- jupyterlab-drawio
- jupyterlab_code_formatter
- jupytext
# PSI specific modules
- jungfrau_utils
- bitshuffle
- sfdata
- pip:
- aquirdturtle_collapsible_headings
- ipytest
# still necessary manually afterwards:
# pip install jupyterlab_hdf
# jupyter labextension install @jupyterlab/hdf5

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name: analysis
channels:
- conda-forge
- defaults
- paulscherrerinstitute
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- anyio=3.5.0=py310h06a4308_0
- appdirs=1.4.4=pyhd3eb1b0_0
- argon2-cffi=21.3.0=pyhd3eb1b0_0
- argon2-cffi-bindings=21.2.0=py310h7f8727e_0
- asttokens=2.0.5=pyhd3eb1b0_0
- attrs=21.4.0=pyhd3eb1b0_0
- babel=2.9.1=pyhd3eb1b0_0
- backcall=0.2.0=pyhd3eb1b0_0
- bitshuffle=0.4.2=py310hc952fd0_0
- black=19.10b0=py_0
- blas=1.0=openblas
- bleach=4.1.0=pyhd3eb1b0_0
- bottleneck=1.3.4=py310h9102076_0
- brotli=1.0.9=he6710b0_2
- brotlipy=0.7.0=py310h7f8727e_1002
- bzip2=1.0.8=h7b6447c_0
- c-ares=1.18.1=h7f8727e_0
- ca-certificates=2022.3.18=h06a4308_0
- cached-property=1.5.2=py_0
- certifi=2021.5.30=py310h06a4308_0
- cffi=1.15.0=py310hd667e15_1
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.4=py310h06a4308_0
- colorama=0.4.4=pyhd3eb1b0_0
- cryptography=36.0.0=py310h9ce1e76_0
- cycler=0.11.0=pyhd3eb1b0_0
- cython=0.29.28=py310h295c915_0
- dbus=1.13.18=hb2f20db_0
- debugpy=1.5.1=py310h295c915_0
- decorator=5.1.1=pyhd3eb1b0_0
- defusedxml=0.7.1=pyhd3eb1b0_0
- entrypoints=0.3=py310h06a4308_0
- executing=0.8.3=pyhd3eb1b0_0
- expat=2.4.4=h295c915_0
- fontconfig=2.13.1=h6c09931_0
- fonttools=4.25.0=pyhd3eb1b0_0
- freetype=2.11.0=h70c0345_0
- giflib=5.2.1=h7b6447c_0
- glib=2.69.1=h4ff587b_1
- gst-plugins-base=1.14.0=h8213a91_2
- gstreamer=1.14.0=h28cd5cc_2
- h5py=3.6.0=nompi_py310he751f51_100
- hdf5=1.12.1=h69dfa17_1
- icu=58.2=he6710b0_3
- idna=3.3=pyhd3eb1b0_0
- importlib-metadata=4.8.2=py310h06a4308_0
- importlib_metadata=4.8.2=hd3eb1b0_0
- iniconfig=1.1.1=pyhd3eb1b0_0
- ipykernel=6.9.1=py310h06a4308_0
- ipympl=0.8.7=pyhd3eb1b0_0
- ipython=8.1.1=py310h06a4308_0
- ipython_genutils=0.2.0=pyhd3eb1b0_1
- ipywidgets=7.6.5=pyhd3eb1b0_1
- jedi=0.18.1=py310h06a4308_1
- jinja2=3.0.3=pyhd3eb1b0_0
- joblib=1.1.0=pyhd3eb1b0_0
- jpeg=9d=h7f8727e_0
- json5=0.9.6=pyhd3eb1b0_0
- jsonschema=3.2.0=py310h06a4308_0
- jungfrau_utils=3.5.0=py_0
- jupyter_client=7.1.2=pyhd3eb1b0_0
- jupyter_core=4.9.2=py310h06a4308_0
- jupyter_server=1.13.5=pyhd3eb1b0_0
- jupyterlab=3.3.2=pyhd3eb1b0_0
- jupyterlab-drawio=0.9.0=pyhd8ed1ab_0
- jupyterlab_code_formatter=1.4.10=pyhd8ed1ab_1
- jupyterlab_pygments=0.1.2=py_0
- jupyterlab_server=2.10.3=pyhd3eb1b0_1
- jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
- jupytext=1.13.7=pyhd0ecf6b_0
- kiwisolver=1.3.1=py310h295c915_0
- krb5=1.19.2=hac12032_0
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.35.1=h7274673_9
- libblas=3.9.0=11_linux64_openblas
- libcblas=3.9.0=11_linux64_openblas
- libcurl=7.80.0=h0b77cf5_0
- libedit=3.1.20210910=h7f8727e_0
- libev=4.33=h7f8727e_1
- libffi=3.3=he6710b0_2
- libgcc-ng=11.2.0=h1d223b6_14
- libgfortran-ng=7.5.0=ha8ba4b0_17
- libgfortran4=7.5.0=ha8ba4b0_17
- libgomp=11.2.0=h1d223b6_14
- liblapack=3.9.0=11_linux64_openblas
- libllvm11=11.1.0=h3826bc1_1
- libnghttp2=1.46.0=hce63b2e_0
- libopenblas=0.3.17=hf726d26_1
- libpng=1.6.37=hbc83047_0
- libsodium=1.0.18=h7b6447c_0
- libssh2=1.9.0=h1ba5d50_1
- libstdcxx-ng=11.2.0=he4da1e4_14
- libtiff=4.2.0=h85742a9_0
- libuuid=1.0.3=h7f8727e_2
- libwebp=1.2.2=h55f646e_0
- libwebp-base=1.2.2=h7f8727e_0
- libxcb=1.14=h7b6447c_0
- libxml2=2.9.12=h03d6c58_0
- llvmlite=0.38.0=py310h4ff587b_0
- lz4-c=1.9.3=h295c915_1
- markdown-it-py=1.1.0=pyhd8ed1ab_0
- markupsafe=2.0.1=py310h7f8727e_0
- matplotlib=3.5.1=py310h06a4308_1
- matplotlib-base=3.5.1=py310ha18d171_1
- matplotlib-inline=0.1.2=pyhd3eb1b0_2
- mdit-py-plugins=0.3.0=pyhd8ed1ab_0
- mistune=0.8.4=py310h7f8727e_1000
- more-itertools=8.12.0=pyhd3eb1b0_0
- munkres=1.1.4=py_0
- mypy_extensions=0.4.3=py310h06a4308_0
- nbclassic=0.3.5=pyhd3eb1b0_0
- nbclient=0.5.11=pyhd3eb1b0_0
- nbconvert=6.1.0=py310h06a4308_0
- nbformat=5.1.3=pyhd3eb1b0_0
- ncurses=6.3=h7f8727e_2
- nest-asyncio=1.5.1=pyhd3eb1b0_0
- notebook=6.4.8=py310h06a4308_0
- numba=0.55.1=py310h00e6091_0
- numexpr=2.7.3=py310hfd7a2a2_1
- numpy=1.21.5=py310h647a097_0
- openssl=1.1.1n=h7f8727e_0
- packaging=21.3=pyhd3eb1b0_0
- pandas=1.4.1=py310h295c915_1
- pandocfilters=1.5.0=pyhd3eb1b0_0
- parso=0.8.3=pyhd3eb1b0_0
- pathspec=0.7.0=py_0
- pcre=8.45=h295c915_0
- pexpect=4.8.0=pyhd3eb1b0_3
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pillow=9.0.1=py310h22f2fdc_0
- pip=21.2.4=py310h06a4308_0
- pluggy=0.13.1=py310h06a4308_0
- prometheus_client=0.13.1=pyhd3eb1b0_0
- prompt-toolkit=3.0.20=pyhd3eb1b0_0
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pure_eval=0.2.2=pyhd3eb1b0_0
- py=1.11.0=pyhd3eb1b0_0
- pycparser=2.21=pyhd3eb1b0_0
- pygments=2.11.2=pyhd3eb1b0_0
- pyopenssl=22.0.0=pyhd3eb1b0_0
- pyparsing=3.0.4=pyhd3eb1b0_0
- pyqt=5.9.2=py310h295c915_6
- pyrsistent=0.18.0=py310h7f8727e_0
- pysocks=1.7.1=py310h06a4308_0
- pytest=6.2.4=py310h06a4308_2
- python=3.10.3=h12debd9_5
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python_abi=3.10=2_cp310
- pytz=2021.3=pyhd3eb1b0_0
- pyzmq=22.3.0=py310h295c915_2
- qt=5.9.7=h5867ecd_1
- readline=8.1.2=h7f8727e_1
- regex=2022.3.15=py310h7f8727e_0
- requests=2.27.1=pyhd3eb1b0_0
- scipy=1.7.3=py310h4f1e569_0
- send2trash=1.8.0=pyhd3eb1b0_1
- setuptools=58.0.4=py310h06a4308_0
- sfdata=0.2.6=py_0
- sip=4.19.13=py310h295c915_0
- six=1.16.0=pyhd3eb1b0_1
- sniffio=1.2.0=py310h06a4308_1
- sqlite=3.38.0=hc218d9a_0
- stack_data=0.2.0=pyhd3eb1b0_0
- tbb=2021.5.0=hd09550d_0
- terminado=0.13.1=py310h06a4308_0
- testpath=0.5.0=pyhd3eb1b0_0
- tk=8.6.11=h1ccaba5_0
- toml=0.10.2=pyhd3eb1b0_0
- tornado=6.1=py310h7f8727e_0
- tqdm=4.63.0=pyhd3eb1b0_0
- traitlets=5.1.1=pyhd3eb1b0_0
- typed-ast=1.4.3=py310h7f8727e_1
- typing-extensions=4.1.1=hd3eb1b0_0
- typing_extensions=4.1.1=pyh06a4308_0
- tzdata=2021e=hda174b7_0
- urllib3=1.26.8=pyhd3eb1b0_0
- wcwidth=0.2.5=pyhd3eb1b0_0
- webencodings=0.5.1=py310h06a4308_1
- websocket-client=0.58.0=py310h06a4308_4
- wheel=0.37.1=pyhd3eb1b0_0
- widgetsnbextension=3.5.2=py310h06a4308_0
- xarray=0.20.1=pyhd3eb1b0_1
- xz=5.2.5=h7b6447c_0
- yaml=0.2.5=h7b6447c_0
- zeromq=4.3.4=h2531618_0
- zipp=3.7.0=pyhd3eb1b0_0
- zlib=1.2.11=h7f8727e_4
- zstd=1.4.9=haebb681_0
- pip:
- aquirdturtle-collapsible-headings==3.1.0
- ipytest==0.12.0
- pyyaml==6.0
prefix: /sf/cristallina/applications/conda/envs/analysis

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eco_test_environment.yml Normal file
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name: cristallina
channels:
- conda-forge
- paulscherrerinstitute
- anaconda
- defaults
dependencies:
# python > 3.8 is currently incompatible with cam_server
- python=3.8
- numpy
- scipy
- ipython
### data science related and not yet covered
# - lmfit
# - scikit-image
# - matplotlib
# - jupyter
# - jupyterlab
# - ipympl
# - nodejs
# - pylint
# - black
# - joblib
# - pint
# - rope
# - dask
# - distributed
# - dask-jobqueue
# - numba
# - pandas
# - pytables
# - openpyxl
# modules required by eco
- colorama
- tabulate
- pyepics
- cam_server
- jungfrau_utils
- lazy-object-proxy
# useful packages for SwissFEL
# - bsread
# - data_api
# - detector_integration_api
# - elog
# - photodiag
# - xrayutilities
# - xraylib
# others
# - tqdm
# - gspread
# - df2gspread
# - oauth2client
# - trackpy
# - pims
# - bitshuffle
- pip
- pip:
- "--editable=git+https://github.com/paulscherrerinstitute/eco.git@6ee2549634294f6015e50025c2aa0d5c8fbf17c6#egg=eco"
#- datastorage
#- plotille
#- uniplot
#- timg
#- tabulate
#- gspread_dataframe
#- gspread_formatting
#- simple-pid
# - git+https://github.com/htlemke/escape-fel@dev
# - git+https://github.com/htlemke/calx
# - git+https://github.com/swissfel/diffcalc3

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slic_explicit_versions.yml Normal file
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name: slic
channels:
- conda-forge
- defaults
- paulscherrerinstitute
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- alsa-lib=1.2.3=h516909a_0
- argon2-cffi=21.3.0=pyhd3eb1b0_0
- argon2-cffi-bindings=21.2.0=py39h7f8727e_0
- asttokens=2.0.5=pyhd3eb1b0_0
- atk-1.0=2.36.0=h28cd5cc_0
- backcall=0.2.0=pyhd3eb1b0_0
- bcrypt=3.2.0=py39he8ac12f_0
- bitshuffle=0.3.6.2=py39h6bb024c_0
- blas=1.0=openblas
- bottleneck=1.3.4=py39hce1f21e_0
- brotli=1.0.9=he6710b0_2
- brotlipy=0.7.0=py39h27cfd23_1003
- bsread=1.5.4=py_0
- ca-certificates=2022.3.18=h06a4308_0
- cairo=1.16.0=hf32fb01_1
- cam_server_client=5.0.6=py39_0
- certifi=2021.10.8=py39h06a4308_2
- cffi=1.15.0=py39hd667e15_1
- charset-normalizer=2.0.4=pyhd3eb1b0_0
- click=8.0.4=py39h06a4308_0
- colorama=0.4.4=pyhd3eb1b0_0
- cryptography=36.0.0=py39h9ce1e76_0
- cycler=0.11.0=pyhd3eb1b0_0
- data_api=0.8.6=py_0
- dataclasses=0.8=pyh6d0b6a4_7
- dbus=1.13.18=hb2f20db_0
- debugpy=1.5.1=py39h295c915_0
- decorator=5.1.1=pyhd3eb1b0_0
- elog=1.3.11=py_0
- entrypoints=0.3=py39h06a4308_0
- epics-base=3.14.12.8=hf484d3e_3
- executing=0.8.3=pyhd3eb1b0_0
- expat=2.4.4=h295c915_0
- font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
- font-ttf-inconsolata=2.001=hcb22688_0
- font-ttf-source-code-pro=2.030=hd3eb1b0_0
- font-ttf-ubuntu=0.83=h8b1ccd4_0
- fontconfig=2.13.1=h6c09931_0
- fonts-anaconda=1=h8fa9717_0
- fonts-conda-ecosystem=1=hd3eb1b0_0
- fonttools=4.25.0=pyhd3eb1b0_0
- freetype=2.11.0=h70c0345_0
- fribidi=1.0.10=h7b6447c_0
- fuzzywuzzy=0.18.0=pyhd8ed1ab_0
- gdk-pixbuf=2.42.6=h04a7f16_0
- gettext=0.21.0=hf68c758_0
- giflib=5.2.1=h7b6447c_0
- glib=2.68.2=h36276a3_0
- gobject-introspection=1.68.0=py39h2109141_1
- graphite2=1.3.14=h23475e2_0
- gst-plugins-base=1.18.4=hf529b03_2
- gstreamer=1.18.4=h76c114f_2
- gtk2=2.24.33=h539f30e_1
- h5py=3.6.0=py39ha0f2276_0
- harfbuzz=2.8.1=h83ec7ef_0
- hdf5=1.10.6=hb1b8bf9_0
- icu=68.1=h2531618_0
- idna=3.3=pyhd3eb1b0_0
- ipykernel=6.9.1=py39h06a4308_0
- ipython=8.1.1=py39h06a4308_0
- jbig=2.1=hdba287a_0
- jedi=0.18.1=py39h06a4308_1
- jpeg=9d=h7f8727e_0
- jungfrau_utils=3.5.0=py_0
- jupyter_client=7.1.2=pyhd3eb1b0_0
- jupyter_core=4.9.2=py39h06a4308_0
- kiwisolver=1.3.2=py39h295c915_0
- krb5=1.19.2=hac12032_0
- lcms2=2.12=h3be6417_0
- ld_impl_linux-64=2.35.1=h7274673_9
- lerc=2.2.1=h2531618_0
- libclang=11.1.0=default_ha53f305_1
- libdeflate=1.7=h27cfd23_5
- libedit=3.1.20210910=h7f8727e_0
- libevent=2.1.10=hcdb4288_3
- libffi=3.3=he6710b0_2
- libgcc-ng=9.3.0=h5101ec6_17
- libgfortran-ng=7.5.0=ha8ba4b0_17
- libgfortran4=7.5.0=ha8ba4b0_17
- libglib=2.68.2=h3e27bee_0
- libglu=9.0.0=hf484d3e_1
- libgomp=9.3.0=h5101ec6_17
- libiconv=1.16=h516909a_0
- libllvm11=11.1.0=h3826bc1_1
- libogg=1.3.5=h27cfd23_1
- libopenblas=0.3.17=hf726d26_1
- libopus=1.3.1=h7b6447c_0
- libpng=1.6.37=hbc83047_0
- libpq=13.3=hd57d9b9_0
- libsodium=1.0.18=h7b6447c_0
- libstdcxx-ng=9.3.0=hd4cf53a_17
- libtiff=4.3.0=hf544144_1
- libuuid=1.0.3=h7f8727e_2
- libvorbis=1.3.7=h7b6447c_0
- libwebp=1.2.2=h55f646e_0
- libwebp-base=1.2.2=h7f8727e_0
- libxcb=1.14=h7b6447c_0
- libxkbcommon=1.0.3=he3ba5ed_0
- libxml2=2.9.12=h72842e0_0
- libxslt=1.1.33=h15afd5d_2
- llvmlite=0.38.0=py39h4ff587b_0
- logzero=1.7.0=py39hf3d152e_1
- lxml=4.6.3=py39h107f48f_0
- lz4-c=1.9.3=h295c915_1
- matplotlib=3.5.1=py39h06a4308_1
- matplotlib-base=3.5.1=py39ha18d171_1
- matplotlib-inline=0.1.2=pyhd3eb1b0_2
- mflow=0.2.0=pyh39e3cac_2
- munkres=1.1.4=py_0
- mysql-common=8.0.25=ha770c72_2
- mysql-libs=8.0.25=hfa10184_2
- ncurses=6.3=h7f8727e_2
- nest-asyncio=1.5.1=pyhd3eb1b0_0
- ninja=1.10.2=py39hd09550d_3
- nspr=4.33=h295c915_0
- nss=3.74=h0370c37_0
- numba=0.55.1=py39h51133e4_0
- numexpr=2.8.1=py39hecfb737_0
- numpy=1.21.2=py39hd8d4704_0
- numpy-base=1.21.2=py39h2b8c604_0
- openssl=1.1.1n=h7f8727e_0
- packaging=21.3=pyhd3eb1b0_0
- pandas=1.4.1=py39h295c915_1
- pango=1.48.5=hb8ff022_0
- parso=0.8.3=pyhd3eb1b0_0
- passlib=1.7.4=pyhd3eb1b0_0
- pathlib2=2.3.6=py39h06a4308_2
- pcre=8.45=h295c915_0
- pexpect=4.8.0=pyhd3eb1b0_3
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pillow=9.0.1=py39h22f2fdc_0
- pip=21.2.4=py39h06a4308_0
- pixman=0.40.0=h7f8727e_1
- prompt-toolkit=3.0.20=pyhd3eb1b0_0
- pthread-stubs=0.3=h0ce48e5_1
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pure_eval=0.2.2=pyhd3eb1b0_0
- pycparser=2.21=pyhd3eb1b0_0
- pyepics=3.4.3=py_0
- pygments=2.11.2=pyhd3eb1b0_0
- pyopenssl=22.0.0=pyhd3eb1b0_0
- pyparsing=3.0.4=pyhd3eb1b0_0
- pypubsub=4.0.3=py_0
- pyqt=5.12.3=py39hf3d152e_7
- pyqt-impl=5.12.3=py39h0fcd23e_7
- pyqt5-sip=4.19.18=py39he80948d_7
- pyqtchart=5.12=py39h0fcd23e_7
- pyqtwebengine=5.12.1=py39h0fcd23e_7
- pysocks=1.7.1=py39h06a4308_0
- python=3.9.11=h12debd9_2
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python-levenshtein=0.12.2=py39h27cfd23_0
- python_abi=3.9=2_cp39
- pytz=2021.3=pyhd3eb1b0_0
- pyzmq=22.3.0=py39h295c915_2
- qt=5.12.9=hda022c4_4
- readline=8.1.2=h7f8727e_1
- requests=2.27.1=pyhd3eb1b0_0
- scipy=1.7.3=py39h492baa0_0
- setuptools=58.0.4=py39h06a4308_0
- sfdata=0.2.6=py_0
- six=1.16.0=pyhd3eb1b0_1
- sqlite=3.38.0=hc218d9a_0
- stack_data=0.2.0=pyhd3eb1b0_0
- tbb=2021.5.0=hd09550d_0
- termcolor=1.1.0=py39h06a4308_1
- tk=8.6.11=h1ccaba5_0
- tornado=6.1=py39h27cfd23_0
- tqdm=4.63.0=pyhd3eb1b0_0
- traitlets=5.1.1=pyhd3eb1b0_0
- typing-extensions=4.1.1=hd3eb1b0_0
- typing_extensions=4.1.1=pyh06a4308_0
- tzdata=2021e=hda174b7_0
- urllib3=1.26.8=pyhd3eb1b0_0
- wcwidth=0.2.5=pyhd3eb1b0_0
- wheel=0.37.1=pyhd3eb1b0_0
- wxpython=4.1.1=py39h09f47c6_1
- xarray=0.20.1=pyhd3eb1b0_1
- xz=5.2.5=h7b6447c_0
- yaspin=2.1.0=pyhd8ed1ab_0
- zeromq=4.3.4=h2531618_0
- zlib=1.2.11=h7f8727e_4
- zstd=1.5.0=ha4553b6_1
prefix: /sf/cristallina/applications/conda/envs/slic