From 35f61d77bb74906d8ca4c36760fd9dcd2074d47e Mon Sep 17 00:00:00 2001 From: James Wrigley Date: Thu, 25 Jul 2024 19:04:34 +0200 Subject: [PATCH 1/6] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 5513ae5f..37099454 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ site/ # Local Netlify folder .netlify +*~ From a71c3de6842072691855110a20793c0caab463d3 Mon Sep 17 00:00:00 2001 From: James Wrigley Date: Thu, 25 Jul 2024 14:22:32 +0200 Subject: [PATCH 2/6] Add uncommitted changes - Added `python-kaleido` - Crystfel 0.9.1 module updated, and 0.11.0 added - MPI changes to the OnDA and smilei modules - Xraylarch module updated - New modules: - bornagain - fiji - glassure - New applications: - imagej - xraylarch --- applications/imagej/environment.lock.yml | 103 +++++ applications/imagej/environment.yml | 7 + applications/xraylarch/environment.lock.yml | 404 ++++++++++++++++++++ applications/xraylarch/environment.yml | 27 ++ environments/202401/1-base.yml | 1 + environments/202401/environment.lock.yml | 2 +- environments/202401/environment.yml | 1 + modules/bornagain/.version | 5 + modules/bornagain/1.19.0 | 18 + modules/crystfel/.version | 3 + modules/crystfel/0.11.0 | 21 + modules/crystfel/0.9.1 | 3 +- modules/exfel_onda/22.11.2-alpha | 7 +- modules/fiji | 13 + modules/glassure/.version | 5 + modules/glassure/1.4.4 | 19 + modules/openmpi-no-python | 23 +- modules/smilei | 10 +- modules/xraylarch | 41 +- 19 files changed, 678 insertions(+), 35 deletions(-) create mode 100644 applications/imagej/environment.lock.yml create mode 100644 applications/imagej/environment.yml create mode 100644 applications/xraylarch/environment.lock.yml create mode 100644 applications/xraylarch/environment.yml create mode 100644 modules/bornagain/.version create mode 100644 modules/bornagain/1.19.0 create mode 100644 modules/crystfel/.version create mode 100644 modules/crystfel/0.11.0 create mode 100644 modules/fiji create mode 100644 modules/glassure/.version create mode 100644 modules/glassure/1.4.4 diff --git a/applications/imagej/environment.lock.yml b/applications/imagej/environment.lock.yml new file mode 100644 index 00000000..06a7deef --- /dev/null +++ b/applications/imagej/environment.lock.yml @@ -0,0 +1,103 @@ +name: pyimagej +channels: + - nodefaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - aom=3.8.2 + - blosc=1.21.5 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - brunsli=0.1 + - bzip2=1.0.8 + - c-blosc2=2.14.3 + - ca-certificates=2024.2.2 + - certifi=2024.2.2 + - charls=2.4.2 + - contourpy=1.2.1 + - cycler=0.12.1 + - dav1d=1.2.1 + - fonttools=4.51.0 + - freetype=2.12.1 + - giflib=5.2.2 + - imagecodecs=2023.9.4 + - imglyb=2.1.0 + - jgo=1.0.5 + - jpype1=1.5.0 + - jxrlib=1.1 + - kiwisolver=1.4.5 + - labeling=0.1.12 + - lcms2=2.15 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libaec=1.1.3 + - libavif16=1.0.4 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcblas=3.9.0 + - libdeflate=1.18 + - libexpat=2.6.2 + - libffi=3.4.2 + - libgcc-ng=13.2.0 + - libgfortran-ng=13.2.0 + - libgfortran5=13.2.0 + - libgomp=13.2.0 + - libjpeg-turbo=2.1.5.1 + - liblapack=3.9.0 + - libnsl=2.0.1 + - libopenblas=0.3.27 + - libpng=1.6.43 + - libsqlite=3.45.2 + - libstdcxx-ng=13.2.0 + - libtiff=4.5.1 + - libuuid=2.38.1 + - libwebp-base=1.3.2 + - libxcb=1.15 + - libxcrypt=4.4.36 + - libzlib=1.2.13 + - libzopfli=1.0.3 + - lz4-c=1.9.4 + - matplotlib-base=3.8.4 + - maven=3.9.6 + - munkres=1.1.4 + - ncurses=6.4.20240210 + - numpy=1.26.4 + - openjdk=8.0.382 + - openjpeg=2.5.0 + - openssl=3.2.1 + - packaging=24.0 + - pandas=2.2.1 + - pillow=9.5.0 + - pip=24.0 + - psutil=5.9.8 + - pthread-stubs=0.4 + - pyimagej=1.4.1 + - pyparsing=3.1.2 + - python=3.11.8 + - python-dateutil=2.9.0 + - python-tzdata=2024.1 + - python_abi=3.11 + - pytz=2024.1 + - rav1e=0.6.6 + - readline=8.2 + - scipy=1.13.0 + - scyjava=1.9.1 + - setuptools=69.2.0 + - six=1.16.0 + - snappy=1.1.10 + - svt-av1=2.0.0 + - tifffile=2024.2.12 + - tk=8.6.13 + - tzdata=2024a + - wheel=0.43.0 + - xarray=2024.3.0 + - xorg-libxau=1.0.11 + - xorg-libxdmcp=1.1.3 + - xz=5.2.6 + - zfp=1.0.1 + - zlib-ng=2.0.7 + - zstd=1.5.5 +prefix: /gpfs/exfel/sw/software/mambaforge/22.11/envs/pyimagej diff --git a/applications/imagej/environment.yml b/applications/imagej/environment.yml new file mode 100644 index 00000000..1c5219c2 --- /dev/null +++ b/applications/imagej/environment.yml @@ -0,0 +1,7 @@ +name: pyimagej +channels: + - nodefaults + - conda-forge +dependencies: + - pyimagej + - openjdk=8 diff --git a/applications/xraylarch/environment.lock.yml b/applications/xraylarch/environment.lock.yml new file mode 100644 index 00000000..965f2fdb --- /dev/null +++ b/applications/xraylarch/environment.lock.yml @@ -0,0 +1,404 @@ +name: xraylarch +channels: + - nodefaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - adwaita-icon-theme=46.2 + - algopy=0.5.7 + - alsa-lib=1.2.11 + - anyio=4.3.0 + - aom=3.9.0 + - argon2-cffi=23.1.0 + - argon2-cffi-bindings=21.2.0 + - arrow=1.3.0 + - asteval=0.9.33 + - asttokens=2.4.1 + - async-lru=2.0.4 + - at-spi2-atk=2.38.0 + - at-spi2-core=2.40.3 + - atk-1.0=2.38.0 + - attr=2.5.1 + - attrs=23.2.0 + - babel=2.14.0 + - beautifulsoup4=4.12.3 + - bleach=6.1.0 + - blosc=1.21.5 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - brotli-python=1.1.0 + - brunsli=0.1 + - bzip2=1.0.8 + - c-ares=1.28.1 + - c-blosc2=2.14.4 + - ca-certificates=2024.6.2 + - cached-property=1.5.2 + - cached_property=1.5.2 + - cairo=1.18.0 + - cchardet=2.1.7 + - certifi=2024.2.2 + - cffi=1.16.0 + - charls=2.4.2 + - charset-normalizer=3.3.2 + - colorama=0.4.6 + - comm=0.2.2 + - cuda-version=12.5 + - cycler=0.12.1 + - dav1d=1.2.1 + - dbus=1.13.6 + - debugpy=1.8.1 + - decorator=5.1.1 + - defusedxml=0.7.1 + - entrypoints=0.4 + - epoxy=1.5.10 + - exceptiongroup=1.2.0 + - executing=2.0.1 + - expat=2.6.2 + - fabio=2024.4.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.53.0 + - fqdn=1.5.1 + - freetype=2.12.1 + - fribidi=1.0.10 + - future=1.0.0 + - gdk-pixbuf=2.42.12 + - gettext=0.22.5 + - gettext-tools=0.22.5 + - giflib=5.2.2 + - glib=2.80.2 + - glib-tools=2.80.2 + - glymur=0.13.2.post1 + - gmp=6.3.0 + - gmpy2=2.1.5 + - graphite2=1.3.13 + - greenlet=3.0.3 + - gst-plugins-base=1.24.4 + - gstreamer=1.24.4 + - gtk3=3.24.42 + - h11=0.14.0 + - h2=4.1.0 + - h5py=3.11.0 + - harfbuzz=8.5.0 + - hdf5=1.14.3 + - hdf5plugin=4.4.0 + - hicolor-icon-theme=0.17 + - hpack=4.0.0 + - httpcore=1.0.5 + - httpx=0.27.0 + - hyperframe=6.0.1 + - icu=73.2 + - idna=3.7 + - imagecodecs=2024.6.1 + - imageio=2.34.1 + - importlib-metadata=7.1.0 + - importlib-resources=6.4.0 + - importlib_metadata=7.1.0 + - importlib_resources=6.4.0 + - iniconfig=2.0.0 + - ipykernel=6.29.3 + - ipympl=0.9.3 + - ipython=8.18.1 + - ipython_genutils=0.2.0 + - ipywidgets=7.7.0 + - isoduration=20.11.0 + - jedi=0.19.1 + - jinja2=3.1.4 + - joblib=1.4.2 + - json5=0.9.25 + - jsonpointer=2.4 + - jsonschema=4.22.0 + - jsonschema-specifications=2023.12.1 + - jsonschema-with-format-nongpl=4.22.0 + - jupyter-lsp=2.2.5 + - jupyter_client=8.6.2 + - jupyter_core=5.7.2 + - jupyter_events=0.10.0 + - jupyter_server=2.14.1 + - jupyter_server_terminals=0.5.3 + - jupyterlab=4.2.1 + - jupyterlab_pygments=0.3.0 + - jupyterlab_server=2.27.2 + - jupyterlab_widgets=1.1.0 + - jxrlib=1.1 + - keyutils=1.6.1 + - kiwisolver=1.4.5 + - krb5=1.21.2 + - lame=3.100 + - latexcodec=2.0.1 + - lazy_loader=0.4 + - lcms2=2.16 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libaec=1.1.3 + - libasprintf=0.22.5 + - libasprintf-devel=0.22.5 + - libavif16=1.0.4 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcap=2.69 + - libcblas=3.9.0 + - libclang-cpp15=15.0.7 + - libclang13=18.1.6 + - libcups=2.3.3 + - libcurl=8.8.0 + - libdeflate=1.20 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.12 + - libexpat=2.6.2 + - libffi=3.4.2 + - libflac=1.4.3 + - libgcc-ng=13.2.0 + - libgcrypt=1.10.3 + - libgettextpo=0.22.5 + - libgettextpo-devel=0.22.5 + - libgfortran-ng=13.2.0 + - libgfortran5=13.2.0 + - libglib=2.80.2 + - libgpg-error=1.49 + - libhwloc=2.10.0 + - libhwy=1.1.0 + - libiconv=1.17 + - libjpeg-turbo=3.0.0 + - libjxl=0.10.2 + - liblapack=3.9.0 + - libllvm15=15.0.7 + - libllvm18=18.1.6 + - libnghttp2=1.58.0 + - libnpp=12.3.0.116 + - libnsl=2.0.1 + - libogg=1.3.4 + - libopus=1.3.1 + - libpng=1.6.43 + - libpq=16.3 + - librsvg=2.58.0 + - libsndfile=1.2.2 + - libsodium=1.0.18 + - libsqlite=3.45.3 + - libssh2=1.11.0 + - libstdcxx-ng=13.2.0 + - libsystemd0=255 + - libtiff=4.6.0 + - libtomo=1.14.4 + - libuuid=2.38.1 + - libvorbis=1.3.7 + - libwebp-base=1.4.0 + - libxcb=1.15 + - libxcrypt=4.4.36 + - libxkbcommon=1.7.0 + - libxml2=2.12.7 + - libxslt=1.1.39 + - libzlib=1.3.1 + - libzopfli=1.0.3 + - llvm-openmp=18.1.6 + - lmfit=1.2.2 + - lxml=5.2.2 + - lz4-c=1.9.4 + - mako=1.3.5 + - markupsafe=2.1.5 + - matplotlib=3.5.2 + - matplotlib-base=3.5.2 + - matplotlib-inline=0.1.3 + - mistune=3.0.2 + - mkl=2023.2.0 + - mkl-service=2.4.1 + - mkl_fft=1.3.10 + - monty=2024.5.24 + - mpc=1.3.1 + - mpfr=4.2.1 + - mpg123=1.32.6 + - mpmath=1.3.0 + - munkres=1.1.4 + - mysql-common=8.3.0 + - mysql-libs=8.3.0 + - nbclient=0.10.0 + - nbconvert-core=7.16.4 + - nbformat=5.10.4 + - ncurses=6.5 + - nest-asyncio=1.6.0 + - networkx=3.2.1 + - notebook=7.2.0 + - notebook-shim=0.2.4 + - nspr=4.35 + - nss=3.100 + - numdifftools=0.9.41 + - numexpr=2.10.0 + - numpy=1.26.4 + - ocl-icd=2.3.2 + - openbabel=3.1.1 + - openjpeg=2.5.2 + - openssl=3.3.1 + - overrides=7.7.0 + - packaging=24.0 + - palettable=3.3.3 + - pandas=2.2.2 + - pandocfilters=1.5.0 + - pango=1.52.2 + - parso=0.8.4 + - patsy=0.5.6 + - pcre2=10.43 + - peakutils=1.3.4 + - pexpect=4.9.0 + - pickleshare=0.7.5 + - pillow=10.3.0 + - pip=24.0 + - pixman=0.43.2 + - pkgutil-resolve-name=1.3.10 + - platformdirs=4.2.2 + - plotly=5.22.0 + - pluggy=1.5.0 + - ply=3.11 + - prometheus_client=0.20.0 + - prompt-toolkit=3.0.46 + - psutil=5.9.8 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - pulseaudio-client=17.0 + - pure_eval=0.2.2 + - pybtex=0.24.0 + - pycifrw=4.4.6 + - pycparser=2.22 + - pyfai=2024.5.0 + - pyfai-base=2024.5.0 + - pygments=2.18.0 + - pymatgen=2024.5.31 + - pyopencl=2024.2.2 + - pyopengl=3.1.6 + - pyparsing=3.1.2 + - pyqt=5.15.9 + - pyqt5-sip=12.12.2 + - pyshortcuts=1.9.0 + - pysocks=1.7.1 + - pytest=8.2.2 + - python=3.9.19 + - python-dateutil=2.9.0 + - python-fastjsonschema=2.19.1 + - python-json-logger=2.0.7 + - python-tzdata=2024.1 + - python_abi=3.9 + - pytools=2024.1.3 + - pytz=2024.1 + - pywavelets=1.4.1 + - pyyaml=6.0.1 + - pyzmq=26.0.3 + - qt-main=5.15.8 + - qtconsole=5.5.2 + - qtconsole-base=5.5.2 + - qtpy=2.4.1 + - rav1e=0.6.6 + - readline=8.2 + - referencing=0.35.1 + - requests=2.32.3 + - rfc3339-validator=0.1.4 + - rfc3986-validator=0.1.1 + - rpds-py=0.18.1 + - ruamel.yaml=0.18.6 + - ruamel.yaml.clib=0.2.8 + - scikit-image=0.22.0 + - scikit-learn=1.5.0 + - scipy=1.13.1 + - send2trash=1.8.3 + - setuptools=70.0.0 + - setuptools-scm=8.1.0 + - silx=2.1.0 + - silx-base=2.1.0 + - sip=6.7.12 + - six=1.16.0 + - snappy=1.2.0 + - sniffio=1.3.1 + - soupsieve=2.5 + - spglib=2.4.0 + - sqlalchemy=2.0.30 + - stack_data=0.6.2 + - statsmodels=0.14.2 + - svt-av1=2.1.0 + - sympy=1.12 + - tabulate=0.9.0 + - tbb=2021.12.0 + - tenacity=8.3.0 + - termcolor=2.4.0 + - terminado=0.18.1 + - threadpoolctl=3.5.0 + - tifffile=2024.5.22 + - tinycss2=1.3.0 + - tk=8.6.13 + - toml=0.10.2 + - tomli=2.0.1 + - tomopy=1.14.4 + - tornado=6.4 + - tqdm=4.66.4 + - traitlets=5.14.3 + - types-python-dateutil=2.9.0.20240316 + - typing-extensions=4.12.1 + - typing_extensions=4.12.1 + - typing_utils=0.1.0 + - tzdata=2024a + - uncertainties=3.2.0 + - unicodedata2=15.1.0 + - uri-template=1.3.0 + - urllib3=2.2.1 + - wayland=1.23.0 + - wcwidth=0.2.13 + - webcolors=24.6.0 + - webencodings=0.5.1 + - websocket-client=1.8.0 + - wheel=0.43.0 + - widgetsnbextension=3.6.6 + - wxmplot=0.9.58 + - wxpython=4.2.1 + - wxutils=0.3.0 + - wxwidgets=3.2.5 + - xcb-util=0.4.0 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.0 + - xcb-util-renderutil=0.3.9 + - xcb-util-wm=0.4.1 + - xkeyboard-config=2.41 + - xorg-compositeproto=0.4.2 + - xorg-damageproto=1.2.1 + - xorg-fixesproto=5.0 + - xorg-inputproto=2.3.2 + - xorg-kbproto=1.0.7 + - xorg-libice=1.1.1 + - xorg-libsm=1.2.4 + - xorg-libx11=1.8.9 + - xorg-libxau=1.0.11 + - xorg-libxcomposite=0.4.6 + - xorg-libxcursor=1.2.0 + - xorg-libxdamage=1.1.5 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxfixes=5.0.3 + - xorg-libxi=1.7.10 + - xorg-libxinerama=1.1.5 + - xorg-libxrandr=1.5.2 + - xorg-libxrender=0.9.11 + - xorg-libxtst=1.2.3 + - xorg-libxxf86vm=1.1.5 + - xorg-randrproto=1.5.0 + - xorg-recordproto=1.14.2 + - xorg-renderproto=0.11.1 + - xorg-util-macros=1.19.3 + - xorg-xextproto=7.3.0 + - xorg-xf86vidmodeproto=2.3.1 + - xorg-xproto=7.0.31 + - xraydb=4.5.0 + - xraylarch=0.9.71 + - xz=5.2.6 + - yaml=0.2.5 + - zeromq=4.3.5 + - zfp=1.0.1 + - zipp=3.17.0 + - zlib=1.3.1 + - zlib-ng=2.0.7 + - zstd=1.5.6 +prefix: /gpfs/exfel/sw/software/mambaforge/22.11/envs/xraylarch diff --git a/applications/xraylarch/environment.yml b/applications/xraylarch/environment.yml new file mode 100644 index 00000000..3a40ccbf --- /dev/null +++ b/applications/xraylarch/environment.yml @@ -0,0 +1,27 @@ +name: xraylarch +channels: + - conda-forge + - nodefaults +dependencies: + - python=3.9 + - fabio + - h5py + - ipympl=0.9.3=pyhd8ed1ab_0 + - ipywidgets=7.7.0=pyhd8ed1ab_0 + - jupyterlab_widgets=1.1.0=pyhd8ed1ab_0 + - matplotlib-base=3.5.2=py39h700656a_0 + - matplotlib-inline=0.1.3=pyhd8ed1ab_0 + - matplotlib=3.5.2=py39hf3d152e_0 + - mkl_fft + - openbabel + - pandas + - plotly + - pycifrw + - pyfai + - pymatgen + - scikit-image + - scikit-learn + - scipy + - tomopy + - wxpython + - xraylarch diff --git a/environments/202401/1-base.yml b/environments/202401/1-base.yml index eb65de8b..17ef9cca 100644 --- a/environments/202401/1-base.yml +++ b/environments/202401/1-base.yml @@ -50,6 +50,7 @@ dependencies: - pyopengl - pyqtgraph - pytest + - python-kaleido - pywavelets - pyzmq<25 - scikit-beam diff --git a/environments/202401/environment.lock.yml b/environments/202401/environment.lock.yml index e0ea6923..137098e8 100644 --- a/environments/202401/environment.lock.yml +++ b/environments/202401/environment.lock.yml @@ -611,5 +611,5 @@ dependencies: - zstd=1.5.5 - pip: - da-utils==0.1.0 - - euxfel-extra==2024.1.1.102+4673431 + - euxfel-extra==2024.1.1.136+bd26a76 prefix: /gpfs/exfel/sw/software/mambaforge/22.11/envs/202401 diff --git a/environments/202401/environment.yml b/environments/202401/environment.yml index b1f4d85e..87d3a1d3 100644 --- a/environments/202401/environment.yml +++ b/environments/202401/environment.yml @@ -77,6 +77,7 @@ dependencies: - pyopengl - pyqtgraph - pytest + - python-kaleido - pywavelets - pyzmq<25 - scikit-beam diff --git a/modules/bornagain/.version b/modules/bornagain/.version new file mode 100644 index 00000000..c131429c --- /dev/null +++ b/modules/bornagain/.version @@ -0,0 +1,5 @@ +#%Module1.0 +## +## The desired version of BornAgain +## +set ModulesVersion "1.19.0" diff --git a/modules/bornagain/1.19.0 b/modules/bornagain/1.19.0 new file mode 100644 index 00000000..2d0bb9c9 --- /dev/null +++ b/modules/bornagain/1.19.0 @@ -0,0 +1,18 @@ +#%Module 1.0 +# +# BornAgain 1.19.0 +# +proc ModulesHelp {} { + puts stdout " " + puts stdout " BornAgain: Open-source research software to simulate and fit neutron and x-ray reflectometry and grazing-incidence small-angle scattering. " + puts stdout " https://jugit.fz-juelich.de/mlz/bornagain " + puts stdout " " +} + +module-whatis "Open-source research software to simulate and fit neutron and x-ray reflectometry and grazing-incidence small-angle scattering." + +if { [ module-info mode load ] } { + system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'bornagain/1.19.0'" +} + +prepend-path PATH /gpfs/exfel/sw/software/xfel_applications/bornagain/bornagain-1.19.0/bin diff --git a/modules/crystfel/.version b/modules/crystfel/.version new file mode 100644 index 00000000..92e2d1d1 --- /dev/null +++ b/modules/crystfel/.version @@ -0,0 +1,3 @@ +#%Module1.0 +# Set default version +set ModulesVersion "0.11.0" diff --git a/modules/crystfel/0.11.0 b/modules/crystfel/0.11.0 new file mode 100644 index 00000000..9b51c557 --- /dev/null +++ b/modules/crystfel/0.11.0 @@ -0,0 +1,21 @@ +#%Module1.0 + +module-whatis "CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data from 'serial crystallography' experiments, often (but not always) performed using an X-ray Free-Electron Laser. " + +proc ModulesHelp { } { + puts stderr "CrystFEL is a suite of programs for processing (and simulating) Bragg" + puts stderr "diffraction data from "serial crystallography" experiments, often (but" + puts stderr "not always) performed using an X-ray Free-Electron Laser. +} + +prepend-path PATH "/gpfs/exfel/sw/software/crystfel/0.11.0/bin" +prepend-path MANPATH "/gpfs/exfel/sw/software/crystfel/0.11.0/share/man" +prepend-path LD_LIBRARY_PATH "/gpfs/exfel/sw/software/crystfel/0.11.0/lib64" +prepend-path LIBRARY_PATH "/gpfs/exfel/sw/software/crystfel/0.11.0/lib64" +prepend-path CPATH "/gpfs/exfel/sw/software/crystfel/0.11.0/include" +prepend-path PKG_CONFIG_PATH "/gpfs/exfel/sw/software/crystfel/0.11.0/lib64/pkgconfig" +prepend-path CMAKE_PREFIX_PATH "/gpfs/exfel/sw/software/crystfel/0.11.0" + +if { [ module-info mode load ] } { + system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'crystfel/0.11.0'" +} diff --git a/modules/crystfel/0.9.1 b/modules/crystfel/0.9.1 index 70c0e16b..f191f4d9 100644 --- a/modules/crystfel/0.9.1 +++ b/modules/crystfel/0.9.1 @@ -16,6 +16,7 @@ proc ModulesHelp { } { if { [ module-info mode load ] } { system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'crystfel/0.9.1'" prepend-path MODULEPATH /gpfs/exfel/sw/software/spack/spack_all/share/spack/modules/linux-centos7-x86_64 - module load ccp4/7.0 + #module load ccp4/7.0 + module load ccp4/8.0 module load crystfel-0.9.1-gcc-8.3.0-ujgzxbx } diff --git a/modules/exfel_onda/22.11.2-alpha b/modules/exfel_onda/22.11.2-alpha index 0a4ecea3..b8dd60b1 100644 --- a/modules/exfel_onda/22.11.2-alpha +++ b/modules/exfel_onda/22.11.2-alpha @@ -20,7 +20,10 @@ if { [module-info mode load] || [module-info mode switch2] } { puts stdout "export JNGFR_CONF=/gpfs/exfel/sw/software/onda_resources/monitor_jf.toml;" # puts stdout "cp -n /gpfs/exfel/sw/software/onda_resources/monitor_agipd.toml . ;" # puts stdout "cp -n /gpfs/exfel/sw/software/onda_resources/monitor_jf.toml . ;" - module load mpi/mpich-3.2-x86_64 + module load exfel openmpi-no-python + puts stdout "export OMPI_MCA_btl=^smcuda" + puts stdout "export OMPI_MCA_rcache=^gpusm,rgpusm" + puts stdout "export OMPI_MCA_accelerator=^cuda" # some issue occured when launching this OnDA version in the SPB hutch # (probably due do a configuration issue of the server) # libGL error: No matching fbConfigs or visuals found @@ -29,7 +32,7 @@ if { [module-info mode load] || [module-info mode switch2] } { puts stdout "export LIBGL_ALWAYS_INDIRECT=1;" } elseif { [module-info mode remove] && ![module-info mode switch3] } { puts stdout "deactivate;" - module unload mpi/mpich-3.2-x86_64 + module unload openmpi-no-python } diff --git a/modules/fiji b/modules/fiji new file mode 100644 index 00000000..85c9752b --- /dev/null +++ b/modules/fiji @@ -0,0 +1,13 @@ +#%Module 1.0 +# +# Modulefile providing imagej via fiji +# +proc ModulesHelp {} { + puts stdout "Modulefile providing imagej via fiji" +} + +module-whatis 'Modulefile providing imagej via fiji' +if { [ module-info mode load ] } { + prepend-path PATH /gpfs/exfel/sw/software/fiji/Fiji.app/bin; +} + diff --git a/modules/glassure/.version b/modules/glassure/.version new file mode 100644 index 00000000..e766d08a --- /dev/null +++ b/modules/glassure/.version @@ -0,0 +1,5 @@ +#%Module1.0 +## +## The desired version of glassure +## +set ModulesVersion "1.4.4" diff --git a/modules/glassure/1.4.4 b/modules/glassure/1.4.4 new file mode 100644 index 00000000..b51ff601 --- /dev/null +++ b/modules/glassure/1.4.4 @@ -0,0 +1,19 @@ +#%Module 1.0 +# +# Glassure 1.4.4 +# +proc ModulesHelp {} { + puts stdout " " + puts stdout " Glassure: An API and GUI program for data analysis of total x-ray diffraction data. " + puts stdout " https://github.com/CPrescher/Glassure " + puts stdout " " +} + +module-whatis "An API and GUI program for data analysis of total x-ray diffraction data." + +if { [ module-info mode load ] } { + system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'glassure/1.4.4'" +} + +prepend-path PATH /gpfs/exfel/sw/software/xfel_applications/glassure/glassure-v1.4.4/bin + diff --git a/modules/openmpi-no-python b/modules/openmpi-no-python index fe2b20f8..7cb6494d 100644 --- a/modules/openmpi-no-python +++ b/modules/openmpi-no-python @@ -6,18 +6,19 @@ conflict mpi if { [ module-info mode load ] } { system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'openmpi-no-python'" - prepend-path PATH /software/openmpi/4.0.3/bin - prepend-path LD_LIBRARY_PATH /software/openmpi/4.0.3/lib - prepend-path PKG_CONFIG_PATH /software/openmpi/4.0.3/lib/pkgconfig - prepend-path MANPATH /software/openmpi/4.0.3/share/man - setenv MPI_BIN /software/openmpi/4.0.3/bin - setenv MPI_SYSCONFIG /software/openmpi/4.0.3/etc - setenv MPI_FORTRAN_MOD_DIR /software/openmpi/4.0.3/lib - setenv MPI_INCLUDE /software/openmpi/4.0.3/include - setenv MPI_LIB /software/openmpi/4.0.3/lib - setenv MPI_MAN /software/openmpi/4.0.3/share/man + prepend-path PATH /software/openmpi/5.0.3/bin + prepend-path LD_LIBRARY_PATH /software/openmpi/5.0.3/lib + prepend-path PKG_CONFIG_PATH /software/openmpi/5.0.3/lib/pkgconfig + prepend-path MANPATH /software/openmpi/5.0.3/share/man + setenv MPI_BIN /software/openmpi/5.0.3/bin + setenv MPI_SYSCONFIG /software/openmpi/5.0.3/etc + setenv MPI_FORTRAN_MOD_DIR /software/openmpi/5.0.3/lib + setenv MPI_INCLUDE /software/openmpi/5.0.3/include + setenv MPI_LIB /software/openmpi/5.0.3/lib + setenv MPI_MAN /software/openmpi/5.0.3/share/man setenv MPI_COMPILER openmpi-x86_64 setenv MPI_SUFFIX _openmpi - setenv MPI_HOME /software/openmpi/4.0.3 + setenv MPI_HOME /software/openmpi/5.0.3 setenv UCX_IB_MLX5_DEVX n + setenv OMPI_MCA_opal_warn_on_missing_libcuda 0 } diff --git a/modules/smilei b/modules/smilei index 97c344a2..48d2a476 100644 --- a/modules/smilei +++ b/modules/smilei @@ -6,13 +6,11 @@ proc ModulesHelp {} { puts stdout "Modulefile providing smilei and py-happi" } +module load mpi + module-whatis 'Modulefile providing smilei and py-happi' if { [ module-info mode load ] } { system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'smilei'" - setenv MPICC /usr/lib64/mpich-3.2/bin/mpicc - setenv MPICXX /usr/lib64/mpich-3.2/bin/mpic++ - setenv MPIF77 /usr/lib64/mpich-3.2/bin/mpif77 - setenv MPIF90 /usr/lib64/mpich-3.2/bin/mpif90 prepend-path ACLOCAL_PATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/share/aclocal; prepend-path CMAKE_PREFIX_PATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view; prepend-path CPATH /gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/python-3.9.13-tkkin3yzgnkx6hou2druate5xauwbktw/include/python3.9; @@ -22,10 +20,6 @@ if { [ module-info mode load ] } { prepend-path PKG_CONFIG_PATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/lib64/pkgconfig:/gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/lib/pkgconfig:/gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/share/pkgconfig; prepend-path PYTHONPATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-six-1.16.0-k75bum5v77ib3sei5odcn7unvalnvvlr/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-pure-eval-0.2.2-iirt3krszawbgzwuhgagc4ivjmhsso2x/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-executing-0.8.2-aq3lvk2ghg3m4oxrmtjifa4372rcn5g7/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-asttokens-2.0.5-xhxg6vsxeex42yjepiysg5hrzsnliysb/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-setuptools-63.0.0-zffnoi65dpbhyyw43b7j33knvyqmyie4/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-wcwidth-0.2.5-wjbohuvvwmhhprdzj2mwkv2zjgcx6blp/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-ptyprocess-0.7.0-7ldo7vwetxrqg4i3sptkyd6wtqwlrmyt/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-traitlets-5.3.0-xudldyrsq6z32mk7yxn5lbhe4yo7spzb/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-parso-0.8.2-62kosdhwc57krictbdk4inncgic76xro/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-typing-extensions-4.3.0-4diacsafkpoeh2flvfyx5popdlvn5kzf/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-tomli-1.2.2-opfnt57rhhsnvffdabbj4xjmprj2lw42/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-platformdirs-2.4.0-kqjoqhycyf3omm6til6si4codjage6h4/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-pathspec-0.9.0-drzt5rcf6c62wln4fc22wq54aiw5fwhm/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-mypy-extensions-0.4.3-fm3xser2pnnucpwlpju52nudncidhrrg/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-click-8.0.3-zxi3jxkbss4edgzkruiniyp34bnfhyp4/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-stack-data-0.2.0-p3noq4pxuomkpaveafvitb5dhfttyyfi/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-pygments-2.10.0-2dmuh6kg55yrv62e4atoynqyiml5hy2c/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-prompt-toolkit-3.0.29-62tyrf56g55uivmm25cwj56yyq6vzxn6/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-pickleshare-0.7.5-22iv6geyfebdy3a2nlxadfqb5bwiqk3c/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-pexpect-4.8.0-gyudosogyq4wdvxvvaemqv65fncgyoib/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-matplotlib-inline-0.1.3-moaukdkuy3sc75h4wccohdhmblstiehs/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-jedi-0.18.1-ph4i4kajpupbimym7a347qyanmf5nyc3/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-decorator-5.1.1-ap275cynepnu55abt3ykwdi4ef5rakxs/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-black-22.6.0-pe6hxal2oq4xzq6uggftopelvfecjxq7/lib/python3.9/site-packages:/gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/py-backcall-0.2.0-dslvgnoemp6jqfbjmayrgoh2b5ehjbc4/lib/python3.9/site-packages } elseif { [module-info mode remove] && ![module-info mode switch3] } { - unsetenv MPICC /usr/lib64/mpich-3.2/bin/mpicc - unsetenv MPICXX /usr/lib64/mpich-3.2/bin/mpic++ - unsetenv MPIF77 /usr/lib64/mpich-3.2/bin/mpif77 - unsetenv MPIF90 /usr/lib64/mpich-3.2/bin/mpif90 remove-path ACLOCAL_PATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view/share/aclocal; remove-path CMAKE_PREFIX_PATH /gpfs/exfel/sw/spack/22.08/var/spack/environments/smilei/.spack-env/view; remove-path CPATH /gpfs/exfel/sw/spack/22.08/opt/spack/linux-centos7-x86_64/gcc-12.1.0/python-3.9.13-tkkin3yzgnkx6hou2druate5xauwbktw/include/python3.9; diff --git a/modules/xraylarch b/modules/xraylarch index 2dd2a5ff..5c409bcc 100644 --- a/modules/xraylarch +++ b/modules/xraylarch @@ -1,6 +1,6 @@ #%Module 1.0 # -# xfel 1.1.1 +# xraylarch # proc ModulesHelp {} { puts stdout " " @@ -8,17 +8,34 @@ proc ModulesHelp {} { puts stdout " " } -module-whatis "Setup environemt for data analysis tools at EuXFEL " +module-whatis "Module loads the xraylarch application" + if { [ module-info mode load ] } { - system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'xraylarch'" - prepend-path PATH /gpfs/exfel/sw/software/xraylarch/bin/ - setenv _CONDA_EXE /gpfs/exfel/sw/software/xraylarch/bin/conda - setenv _CONDA_ROOT /gpfs/exfel/sw/software/xraylarch/bin/ - setenv OPENCL_VENDOR_PATH /etc/OpenCL/vendors -} elseif { [module-info mode remove] && ![module-info mode switch3] } { - remove-path PATH /gpfs/exfel/sw/software/xraylarch/bin - unsetenv _CONDA_EXE - unsetenv _CONDA_ROOT - unsetenv OPENCL_VENDOR_PATH + system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'xraylarch'" } +module load mambaforge + +prepend-path PATH /gpfs/exfel/sw/software/mambaforge/22.11/envs/xraylarch/bin +prepend-path XML_CATALOG_FILES file {///gpfs/exfel/sw/software/mambaforge/22.11/envs/xraylarch/etc/xml/catalog file} ///etc/xml/catalog +setenv CONDA_DEFAULT_ENV xraylarch +setenv CONDA_PREFIX /gpfs/exfel/sw/software/mambaforge/22.11/envs/xraylarch +setenv CONDA_PROMPT_MODIFIER {(xraylarch) } +setenv CONDA_SHLVL 1 +setenv GSETTINGS_SCHEMA_DIR /gpfs/exfel/sw/software/mambaforge/22.11/envs/xraylarch/share/glib-2.0/schemas +setenv GSETTINGS_SCHEMA_DIR_CONDA_BACKUP {} + +#module-whatis "Setup environemt for data analysis tools at EuXFEL " +#if { [ module-info mode load ] } { +# system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'xraylarch'" +# prepend-path PATH /gpfs/exfel/sw/software/xraylarch/bin/ +# setenv _CONDA_EXE /gpfs/exfel/sw/software/xraylarch/bin/conda +# setenv _CONDA_ROOT /gpfs/exfel/sw/software/xraylarch/bin/ +# setenv OPENCL_VENDOR_PATH /etc/OpenCL/vendors +#} elseif { [module-info mode remove] && ![module-info mode switch3] } { +# remove-path PATH /gpfs/exfel/sw/software/xraylarch/bin +# unsetenv _CONDA_EXE +# unsetenv _CONDA_ROOT +# unsetenv OPENCL_VENDOR_PATH +#} + From 3556dcac06ff5500679ab4ba1ed9c99163f689f2 Mon Sep 17 00:00:00 2001 From: James Wrigley Date: Thu, 25 Jul 2024 18:52:44 +0200 Subject: [PATCH 3/6] Update DAMNIT --- custom-recipes/recipes/damnit/recipe.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/custom-recipes/recipes/damnit/recipe.yaml b/custom-recipes/recipes/damnit/recipe.yaml index 0d4735a9..e4aae5f2 100644 --- a/custom-recipes/recipes/damnit/recipe.yaml +++ b/custom-recipes/recipes/damnit/recipe.yaml @@ -1,6 +1,6 @@ context: name: damnit - version: '0.1.2' + version: '0.1.3' package: name: '{{ name|lower }}' @@ -24,7 +24,9 @@ requirements: - python >=3.9 - h5netcdf - h5py + - orjson - pandas + - plotly - xarray test: From cb07e60a5c93edab856e702dc3776efb9a01e666 Mon Sep 17 00:00:00 2001 From: James Wrigley Date: Thu, 25 Jul 2024 18:53:52 +0200 Subject: [PATCH 4/6] Update the docs for managing environments and building recipes The makefile instructions for building recipes have been deleted entirely because that whole thing has been broken for a while. --- docs/maintenance/environments.md | 5 +++-- docs/maintenance/recipes.md | 17 ++--------------- scripts/utility.py | 2 +- 3 files changed, 6 insertions(+), 18 deletions(-) diff --git a/docs/maintenance/environments.md b/docs/maintenance/environments.md index 591cc89e..f1963dab 100644 --- a/docs/maintenance/environments.md +++ b/docs/maintenance/environments.md @@ -60,7 +60,8 @@ Now, `cd` into the directory of the environment you are working on (e.g. `cd ./e This will merge all of the individual environment files into a single `environment.yml` file which can then be used to create/update an environment. -The command will print off instructions on what to do next: +The command will print off instructions on what to do next, which will look +something like: > Next steps: > @@ -70,7 +71,7 @@ The command will print off instructions on what to do next: > > For an existing environment, update it via: > -> mamba update --no-update-deps -n 202302 -f ./environment.yml +> mamba update --no-update-deps -n 202302 -c ../../custom-recipes/conda-bld -f ./environment.yml > > After update/install is complete create a 'lock file' by running export: > diff --git a/docs/maintenance/recipes.md b/docs/maintenance/recipes.md index fe02dd60..00510279 100644 --- a/docs/maintenance/recipes.md +++ b/docs/maintenance/recipes.md @@ -105,21 +105,7 @@ You should change the source to be the git repository URL, and add information f ## Building the Recipes -Once a new recipe is created, it must be built to create an installable package. A Makefile is provided for ease of use, the Makefile will run the build commands in a container, and builds are done in a temporary shared memory directory to improve performance. Build outputs are stored in the `conda-bld` directory. - -You can use the Makefile to build all recipes, or a single recipe: - -```sh -# Inside the `custom-recipes` directory -make build # Build all recipes -make build PKG=extra-data # Build a single recipe -``` - -!!! note - - The Makefile has a bit of logic to figure out if it is running on a shared node on Maxwell. If it is then it will run the docker command via `srun` (as docker only works on dedicated nodes, not shared nodes). If it is not then it will just use `docker` directly. - -If there are issues during the build then you can troubleshoot the process by running the commands manually: +Once a new recipe is created, it must be built to create an installable package. ```sh # Activate the correct environment when on xsoft@maxwell @@ -130,6 +116,7 @@ mamba activate base boa build \ --skip-existing \ --target-platform linux-64 \ + --output-folder ./conda-bld ./recipes/$PACKAGE # Optional package name # Once the build is complete, index the build directory diff --git a/scripts/utility.py b/scripts/utility.py index 56980136..8ccd8937 100755 --- a/scripts/utility.py +++ b/scripts/utility.py @@ -114,7 +114,7 @@ def merge_environment_files(files: List[str], name: str): For an existing environment, update it via: - mamba update --no-update-deps -n {name} -f ./environment.yml + mamba update --no-update-deps -n {name} -c ../../custom-recipes/conda-bld -f ./environment.yml After update/install is complete create a 'lock file' by running export: From 98a968887e69ac72b7cf88fb841c58aa9d644e2b Mon Sep 17 00:00:00 2001 From: JamesWrigley Date: Mon, 15 Jul 2024 15:46:40 +0200 Subject: [PATCH 5/6] Install the 202402 environment --- environments/202402/0-desy-pinned.yml | 37 ++ environments/202402/1-base.yml | 75 +++ environments/202402/2-custom.yml | 26 + environments/202402/README.md | 10 + environments/202402/environment.lock.yml | 632 +++++++++++++++++++++++ environments/202402/environment.yml | 107 ++++ modules/exfel-python/202402 | 22 + 7 files changed, 909 insertions(+) create mode 100644 environments/202402/0-desy-pinned.yml create mode 100644 environments/202402/1-base.yml create mode 100644 environments/202402/2-custom.yml create mode 100644 environments/202402/README.md create mode 100644 environments/202402/environment.lock.yml create mode 100644 environments/202402/environment.yml create mode 100644 modules/exfel-python/202402 diff --git a/environments/202402/0-desy-pinned.yml b/environments/202402/0-desy-pinned.yml new file mode 100644 index 00000000..fd3a829c --- /dev/null +++ b/environments/202402/0-desy-pinned.yml @@ -0,0 +1,37 @@ +name: desy-pinned +channels: + - conda-forge + - nodefaults +dependencies: + - brotlipy=0.7.0=py39hb9d737c_1004 + - certipy=0.1.3=py_0 + - ipykernel=6.13.1=py39hef51801_0 + - ipympl=0.9.3=pyhd8ed1ab_0 + - ipython=7.33.0=py39hf3d152e_0 + - ipython_genutils=0.2.0=py_1 + - ipywidgets=7.7.0=pyhd8ed1ab_0 + - jupyter=1.0.0=py39hf3d152e_7 + - jupyter-resource-usage=0.7.1=pyhd8ed1ab_0 + - jupyter-server-mathjax=0.2.6=pyh5bfe37b_1 + - jupyter-server-proxy=4.1.0=pyhd8ed1ab_0 + - jupyter_client=7.3.4=pyhd8ed1ab_0 + - jupyter_console=6.4.3=pyhd8ed1ab_0 + - jupyter_core=4.10.0=py39hf3d152e_0 + - jupyter_server=1.17.1=pyhd8ed1ab_0 + - jupyter_telemetry=0.1.0=pyhd8ed1ab_1 + - jupyterhub=2.3.1=pyhd8ed1ab_0 + - jupyterhub-base=2.3.1=pyhd8ed1ab_0 + - jupyterlab=3.4.3=pyhd8ed1ab_0 + - jupyterlab-git=0.41.0=pyhd8ed1ab_1 + - jupyterlab-h5web=7.0.0=pyhd8ed1ab_0 + - jupyterlab_code_formatter=1.6.0=pyhd8ed1ab_0 + - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0 + - jupyterlab_server=2.14.0=pyhd8ed1ab_0 + - jupyterlab_widgets=1.1.0=pyhd8ed1ab_0 + - matplotlib=3.5.2=py39hf3d152e_0 + - matplotlib-base=3.5.2=py39h700656a_0 + - matplotlib-inline=0.1.3=pyhd8ed1ab_0 + - pyls-spyder=0.4.0=pyhd8ed1ab_0 + - scipy=1.8.1=py39he49c0e8_0 + - spyder=5.3.1=py39hf3d152e_0 + - spyder-kernels=2.3.1=py39hf3d152e_0 diff --git a/environments/202402/1-base.yml b/environments/202402/1-base.yml new file mode 100644 index 00000000..7297a07d --- /dev/null +++ b/environments/202402/1-base.yml @@ -0,0 +1,75 @@ +channels: + - nodefaults + - conda-forge +dependencies: + - python=3.10 + + # No clue why, but mamba errors when these pytorch dependencies are + # present. For now we create the environment.yml file without them and install + # them manually: + # $ module load exfel mambaforge + # $ mamba activate 202402 + # $ mamba install pytorch torchvision torchaudio cpuonly -c pytorch + # - cpuonly::pytorch + # - pytorch::pytorch + # - torchaudio::pytorch + # - torchvision::pytorch + + - astropy + - bokeh + - curl + - cython + - dask + - dask-jobqueue + - dask-labextension + - datashader + - fabio + - fast-histogram + - fftw + - h5glance>=0.8.1 + - h5netcdf + - h5py + - hvplot + - imageio + - iminuit + - ipympl + - ipython + - ipywidgets + - jupyter + - jupyterlab + - jupyterlab-lsp + - kafka-python-ng + - lmfit + - matplotlib + - mpl-interactions + - msgpack-numpy + - msgpack-python + - natsort + - netcdf4 + - numba + - numpy + - opencv + - papermill + - pint + - plotly + - polars + - pyabel + - pybaselines + - pyfai + - pyopengl + - pyqtgraph + - pytest + - python-kaleido + - pywavelets + # We need to use an older pyzmq version until Maxwell updates + # to jupyter-client v8: https://github.com/spyder-ide/spyder/issues/20381 + - pyzmq<25 + - scikit-beam + - scikit-image + - scikit-learn + - scipy + - seaborn + - silx + - spyder + - xarray + - xraylib diff --git a/environments/202402/2-custom.yml b/environments/202402/2-custom.yml new file mode 100644 index 00000000..7f556431 --- /dev/null +++ b/environments/202402/2-custom.yml @@ -0,0 +1,26 @@ +channels: + - nodefaults + - file://gpfs/exfel/sw/software/euxfel-environment-management/custom-recipes/conda-bld + - conda-forge +dependencies: + - calibration-client >=11.3.0 + - cfelpyutils + - condat-gridconv + - damnit + - envmodules + - euxfel-bunch-pattern + - extra-data >= 1.14 + - extra-geom + - extra-hed + - findxfel + - hdf5-vds-check + - karabo-bridge + - karabo_bridge_recorder + - matplotlib-scalebar + - metadata-client + - metropc + - nbclick + - pasha + - princess + - condor +category: custom diff --git a/environments/202402/README.md b/environments/202402/README.md new file mode 100644 index 00000000..39d32eec --- /dev/null +++ b/environments/202402/README.md @@ -0,0 +1,10 @@ +# 202402 Environment + +## Added + +- kafka-python-ng + + +## Removed + +- kafka-python diff --git a/environments/202402/environment.lock.yml b/environments/202402/environment.lock.yml new file mode 100644 index 00000000..16a53743 --- /dev/null +++ b/environments/202402/environment.lock.yml @@ -0,0 +1,632 @@ +name: '202402' +channels: + - pytorch + - file:///gpfs/exfel/sw/software/euxfel-environment-management/custom-recipes/conda-bld + - nodefaults + - conda-forge +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - aiohttp=3.9.5 + - aiosignal=1.3.1 + - alabaster=0.7.16 + - alembic=1.13.2 + - alsa-lib=1.2.9 + - ansicolors=1.1.8 + - anyio=3.7.1 + - aom=3.7.1 + - appdirs=1.4.4 + - argon2-cffi=23.1.0 + - argon2-cffi-bindings=21.2.0 + - arrow=1.3.0 + - astcheck=0.4.0 + - asteval=1.0.1 + - astroid=3.2.4 + - astropy=6.1.2 + - astropy-iers-data=0.2024.7.22.0.34.13 + - async-timeout=4.0.3 + - async_generator=1.10 + - atomicwrites=1.4.1 + - attr=2.5.1 + - attrs=23.2.0 + - autopep8=1.6.0 + - aws-c-auth=0.7.4 + - aws-c-cal=0.6.2 + - aws-c-common=0.9.3 + - aws-c-compression=0.2.17 + - aws-c-event-stream=0.3.2 + - aws-c-http=0.7.13 + - aws-c-io=0.13.32 + - aws-c-mqtt=0.9.6 + - aws-c-s3=0.3.17 + - aws-c-sdkutils=0.1.12 + - aws-checksums=0.1.17 + - aws-crt-cpp=0.23.1 + - aws-sdk-cpp=1.11.156 + - babel=2.14.0 + - backcall=0.2.0 + - backports=1.0 + - backports.tarfile=1.0.0 + - beautifulsoup4=4.12.3 + - binaryornot=0.4.4 + - black=24.4.2 + - bleach=6.1.0 + - blinker=1.8.2 + - blosc=1.21.5 + - bokeh=3.5.0 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - brotli-python=1.1.0 + - brotlipy=0.7.0 + - brunsli=0.1 + - bzip2=1.0.8 + - c-ares=1.32.3 + - c-blosc2=2.12.0 + - ca-certificates=2024.7.4 + - cached-property=1.5.2 + - cached_property=1.5.2 + - cairo=1.16.0 + - calibration-client=11.3.0 + - certifi=2024.7.4 + - certipy=0.1.3 + - cfelpyutils=2.0.6 + - cffi=1.16.0 + - cftime=1.6.4 + - chardet=5.2.0 + - charls=2.4.2 + - charset-normalizer=3.3.2 + - click=8.1.7 + - cloudpickle=3.0.0 + - colorama=0.4.6 + - colorcet=3.1.0 + - condat-gridconv=latest + - condor=1.0.7 + - configurable-http-proxy=4.6.0 + - contourpy=1.2.1 + - cookiecutter=2.6.0 + - cpuonly=2.0 + - cryptography=42.0.2 + - curl=8.4.0 + - cycler=0.12.1 + - cython=3.0.10 + - cytoolz=0.12.3 + - damnit=0.1.3 + - dask=2024.7.1 + - dask-core=2024.7.1 + - dask-expr=1.1.9 + - dask-jobqueue=0.8.5 + - dask-labextension=6.2.0 + - datashader=0.16.3 + - dav1d=1.2.1 + - dbus=1.13.6 + - debugpy=1.8.2 + - decorator=5.1.1 + - defusedxml=0.7.1 + - diff-match-patch=20230430 + - dill=0.3.8 + - distributed=2024.7.1 + - docutils=0.21.2 + - entrypoints=0.4 + - envmodules=0.1 + - euxfel-bunch-pattern=0.6 + - exceptiongroup=1.2.2 + - expat=2.6.2 + - extra-data=1.17.0 + - extra-geom=1.12.0 + - extra-hed=0.1.0 + - fabio=2024.4.0 + - fast-histogram=0.14 + - ffmpeg=6.1.0 + - fftw=3.3.10 + - filelock=3.15.4 + - findxfel=0.1.1 + - flake8=4.0.1 + - flexcache=0.3 + - flexparser=0.3.1 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.14.2 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.53.1 + - freeglut=3.2.2 + - freetype=2.12.1 + - fribidi=1.0.10 + - frozenlist=1.4.1 + - fsspec=2024.6.1 + - future=1.0.0 + - gettext=0.22.5 + - gettext-tools=0.22.5 + - gflags=2.2.2 + - giflib=5.2.2 + - gitdb=4.0.11 + - gitpython=3.1.43 + - glib=2.80.2 + - glib-tools=2.80.2 + - glog=0.6.0 + - glymur=0.13.4 + - gmp=6.3.0 + - gmpy2=2.1.5 + - gnutls=3.7.9 + - graphite2=1.3.13 + - greenlet=3.0.3 + - gsl=2.7 + - gst-plugins-base=1.22.5 + - gstreamer=1.22.5 + - h2=4.1.0 + - h5glance=0.8.1 + - h5grove=1.2.0 + - h5netcdf=1.3.0 + - h5py=3.9.0 + - harfbuzz=7.3.0 + - hdf4=4.2.15 + - hdf5=1.14.1 + - hdf5-vds-check=1.0 + - hdf5plugin=4.1.3 + - holoviews=1.12.7 + - hpack=4.0.0 + - htmlgen=2.0.0 + - hvplot=0.8.1 + - hyperframe=6.0.1 + - icu=72.1 + - idna=3.7 + - imagecodecs=2023.9.4 + - imageio=2.34.2 + - imagesize=1.4.1 + - iminuit=2.26.0 + - importlib-metadata=8.2.0 + - importlib_metadata=8.2.0 + - importlib_resources=6.4.0 + - inflection=0.5.1 + - iniconfig=2.0.0 + - intervaltree=3.1.0 + - ipykernel=6.13.1 + - ipympl=0.9.3 + - ipython=7.33.0 + - ipython_genutils=0.2.0 + - ipywidgets=7.7.0 + - isort=5.13.2 + - jaraco.classes=3.4.0 + - jaraco.context=5.3.0 + - jaraco.functools=4.0.0 + - jasper=4.0.0 + - jedi=0.18.2 + - jeepney=0.8.0 + - jellyfish=1.0.4 + - jinja2=3.1.4 + - joblib=1.4.2 + - json5=0.9.25 + - jsonschema=4.23.0 + - jsonschema-specifications=2023.12.1 + - jupyter=1.0.0 + - jupyter-lsp=2.2.5 + - jupyter-resource-usage=0.7.1 + - jupyter-server-mathjax=0.2.6 + - jupyter-server-proxy=4.1.0 + - jupyter_client=7.3.4 + - jupyter_console=6.4.3 + - jupyter_core=4.10.0 + - jupyter_server=1.17.1 + - jupyter_telemetry=0.1.0 + - jupyterhub=2.3.1 + - jupyterhub-base=2.3.1 + - jupyterlab=3.4.3 + - jupyterlab-git=0.41.0 + - jupyterlab-h5web=7.0.0 + - jupyterlab-lsp=3.10.2 + - jupyterlab_code_formatter=1.6.0 + - jupyterlab_pygments=0.2.2 + - jupyterlab_server=2.14.0 + - jupyterlab_widgets=1.1.0 + - jxrlib=1.1 + - kafka-python-ng=2.2.2 + - kaleido-core=0.2.1 + - karabo-bridge=0.7.0 + - karabo_bridge_recorder=0.2 + - keyring=25.2.1 + - keyutils=1.6.1 + - kiwisolver=1.4.5 + - krb5=1.21.2 + - lame=3.100 + - lazy_loader=0.4 + - lcms2=2.15 + - ld_impl_linux-64=2.40 + - lerc=4.0.0 + - libabseil=20230125.3 + - libaec=1.1.3 + - libarrow=13.0.0 + - libasprintf=0.22.5 + - libasprintf-devel=0.22.5 + - libass=0.17.1 + - libavif16=1.0.3 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcap=2.69 + - libcblas=3.9.0 + - libclang=15.0.7 + - libclang13=15.0.7 + - libcrc32c=1.1.2 + - libcups=2.3.3 + - libcurl=8.4.0 + - libdeflate=1.18 + - libdrm=2.4.122 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.12 + - libexpat=2.6.2 + - libffi=3.4.2 + - libflac=1.4.3 + - libgcc-ng=14.1.0 + - libgcrypt=1.11.0 + - libgettextpo=0.22.5 + - libgettextpo-devel=0.22.5 + - libgfortran-ng=14.1.0 + - libgfortran5=14.1.0 + - libglib=2.80.2 + - libglu=9.0.0 + - libgomp=14.1.0 + - libgoogle-cloud=2.12.0 + - libgpg-error=1.50 + - libgrpc=1.56.2 + - libhwloc=2.9.3 + - libiconv=1.17 + - libidn2=2.3.7 + - libjpeg-turbo=2.1.5.1 + - liblapack=3.9.0 + - liblapacke=3.9.0 + - libllvm14=14.0.6 + - libllvm15=15.0.7 + - libnetcdf=4.9.2 + - libnfft=3.5.3 + - libnghttp2=1.58.0 + - libnsl=2.0.1 + - libnuma=2.0.18 + - libogg=1.3.5 + - libopenblas=0.3.25 + - libopencv=4.8.0 + - libopenvino=2023.0.1 + - libopenvino-auto-batch-plugin=2023.0.1 + - libopenvino-auto-plugin=2023.0.1 + - libopenvino-hetero-plugin=2023.0.1 + - libopenvino-intel-cpu-plugin=2023.0.1 + - libopenvino-intel-gpu-plugin=2023.0.1 + - libopenvino-ir-frontend=2023.0.1 + - libopenvino-onnx-frontend=2023.0.1 + - libopenvino-paddle-frontend=2023.0.1 + - libopenvino-pytorch-frontend=2023.0.1 + - libopenvino-tensorflow-frontend=2023.0.1 + - libopenvino-tensorflow-lite-frontend=2023.0.1 + - libopus=1.3.1 + - libpciaccess=0.18 + - libpng=1.6.43 + - libpq=15.4 + - libprotobuf=4.23.3 + - libsndfile=1.2.2 + - libsodium=1.0.18 + - libspatialindex=2.0.0 + - libspimage=1.0.0 + - libsqlite=3.46.0 + - libssh2=1.11.0 + - libstdcxx-ng=14.1.0 + - libsystemd0=255 + - libtasn1=4.19.0 + - libthrift=0.19.0 + - libtiff=4.5.1 + - libunistring=0.9.10 + - libutf8proc=2.8.0 + - libuuid=2.38.1 + - libuv=1.46.0 + - libva=2.21.0 + - libvorbis=1.3.7 + - libvpx=1.13.1 + - libwebp=1.3.1 + - libwebp-base=1.3.1 + - libxcb=1.15 + - libxkbcommon=1.6.0 + - libxml2=2.11.5 + - libxslt=1.1.37 + - libzip=1.10.1 + - libzlib=1.2.13 + - libzopfli=1.0.3 + - llvmlite=0.42.0 + - lmfit=1.3.2 + - locket=1.0.0 + - lxml=4.9.3 + - lz4=4.3.3 + - lz4-c=1.9.4 + - mako=1.3.5 + - markdown-it-py=3.0.0 + - markupsafe=2.1.5 + - mathjax=2.7.7 + - matplotlib=3.5.2 + - matplotlib-base=3.5.2 + - matplotlib-inline=0.1.3 + - matplotlib-scalebar=0.8.1 + - mccabe=0.6.1 + - mdurl=0.1.2 + - metadata-client=3.9.0 + - metropc=1.4.1 + - mistune=3.0.2 + - more-itertools=10.3.0 + - mpc=1.3.1 + - mpfr=4.2.1 + - mpg123=1.32.6 + - mpl-interactions=0.24.1 + - mpmath=1.3.0 + - msgpack-numpy=0.4.8 + - msgpack-python=1.0.8 + - multidict=6.0.5 + - multipledispatch=0.6.0 + - munkres=1.1.4 + - mypy_extensions=1.0.0 + - mysql-common=8.0.33 + - mysql-libs=8.0.33 + - natsort=8.4.0 + - nbclassic=0.5.6 + - nbclick=0.4.1 + - nbclient=0.7.0 + - nbconvert=7.16.4 + - nbconvert-core=7.16.4 + - nbconvert-pandoc=7.16.4 + - nbdime=3.2.1 + - nbformat=5.10.3 + - nbparameterise=0.6 + - ncurses=6.5 + - nest-asyncio=1.6.0 + - netcdf4=1.6.4 + - nettle=3.9.1 + - networkx=3.2 + - nodejs=18.17.1 + - nomkl=1.0 + - notebook=6.5.7 + - notebook-shim=0.2.4 + - nspr=4.35 + - nss=3.100 + - numba=0.59.1 + - numexpr=2.10.0 + - numpy=1.24.4 + - numpydoc=1.7.0 + - oauth2-xfel-client=6.1.0 + - oauthlib=3.2.2 + - ocl-icd=2.3.2 + - ocl-icd-system=1.0.0 + - opencv=4.8.0 + - openh264=2.3.1 + - openjpeg=2.5.0 + - openssl=3.1.6 + - orc=1.9.0 + - orjson=3.10.6 + - p11-kit=0.24.1 + - packaging=24.1 + - pamela=1.1.0 + - pandas=2.2.2 + - pandoc=3.2.1 + - pandocfilters=1.5.0 + - papermill=2.6.0 + - param=1.13.0 + - parso=0.8.4 + - partd=1.4.2 + - pasha=0.1.1 + - pathspec=0.12.1 + - patsy=0.5.6 + - pcre2=10.43 + - pexpect=4.9.0 + - pickleshare=0.7.5 + - pillow=10.0.0 + - pint=0.24.3 + - pip=24.0 + - pixman=0.43.2 + - pkgutil-resolve-name=1.3.10 + - platformdirs=4.2.2 + - plotly=5.23.0 + - pluggy=1.5.0 + - ply=3.11 + - polars=1.2.1 + - princess=0.6 + - prometheus_client=0.20.0 + - prompt-toolkit=3.0.47 + - prompt_toolkit=3.0.47 + - psutil=6.0.0 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - pugixml=1.13 + - pulseaudio-client=16.1 + - py-opencv=4.8.0 + - pyabel=0.9.0 + - pyarrow=13.0.0 + - pyarrow-hotfix=0.6 + - pybaselines=1.1.0 + - pycodestyle=2.8.0 + - pycparser=2.22 + - pyct=0.5.0 + - pycurl=7.45.1 + - pydocstyle=6.3.0 + - pyerfa=2.0.1.4 + - pyfai=2024.5.0 + - pyfai-base=2024.5.0 + - pyflakes=2.4.0 + - pygments=2.18.0 + - pyjwt=2.8.0 + - pylint=3.2.6 + - pyls-spyder=0.4.0 + - pyopencl=2024.2.7 + - pyopengl=3.1.6 + - pyopenssl=24.2.1 + - pyparsing=3.1.2 + - pyqt=5.15.9 + - pyqt5-sip=12.12.2 + - pyqtgraph=0.13.7 + - pyqtwebengine=5.15.9 + - pysocks=1.7.1 + - pytest=8.3.1 + - python=3.10.13 + - python-dateutil=2.9.0 + - python-fastjsonschema=2.20.0 + - python-json-logger=2.0.7 + - python-kaleido=0.2.1 + - python-lsp-black=2.0.0 + - python-lsp-jsonrpc=1.1.2 + - python-lsp-server=1.4.1 + - python-slugify=8.0.4 + - python-tzdata=2024.1 + - python_abi=3.10 + - pytoolconfig=1.2.5 + - pytools=2024.1.11 + - pytorch=2.0.0 + - pytorch-mutex=1.0 + - pytz=2024.1 + - pyviz_comms=2.3.2 + - pywavelets=1.6.0 + - pyxdg=0.28 + - pyyaml=6.0.1 + - pyzmq=24.0.1 + - qdarkstyle=3.0.3 + - qstylizer=0.2.3 + - qt-main=5.15.8 + - qt-webengine=5.15.8 + - qtawesome=1.3.1 + - qtconsole=5.3.2 + - qtconsole-base=5.3.2 + - qtpy=2.4.1 + - rav1e=0.6.6 + - rdma-core=28.9 + - re2=2023.03.02 + - readline=8.2 + - referencing=0.35.1 + - requests=2.32.3 + - requests-oauthlib=2.0.0 + - rich=13.7.1 + - rope=1.13.0 + - rpds-py=0.19.1 + - rtree=1.3.0 + - ruamel.yaml=0.18.6 + - ruamel.yaml.clib=0.2.8 + - s2n=1.3.54 + - scikit-beam=0.0.26 + - scikit-image=0.24.0 + - scikit-learn=1.5.1 + - scipy=1.8.1 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - secretstorage=3.3.3 + - send2trash=1.8.3 + - setuptools=71.0.4 + - setuptools-scm=8.1.0 + - silx=2.1.0 + - silx-base=2.1.0 + - simpervisor=1.0.0 + - sip=6.7.12 + - siphash24=1.6 + - six=1.16.0 + - sleef=3.6.1 + - smmap=5.0.0 + - snappy=1.1.10 + - sniffio=1.3.1 + - snowballstemmer=2.2.0 + - sortedcontainers=2.4.0 + - soupsieve=2.5 + - sphinx=7.4.7 + - sphinxcontrib-applehelp=1.0.8 + - sphinxcontrib-devhelp=1.0.6 + - sphinxcontrib-htmlhelp=2.0.6 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.8 + - sphinxcontrib-serializinghtml=1.1.10 + - spsim=1.0.0 + - spyder=5.3.1 + - spyder-kernels=2.3.1 + - sqlalchemy=2.0.31 + - sqlite=3.46.0 + - statsmodels=0.14.2 + - svt-av1=1.7.0 + - sympy=1.13.0 + - tabulate=0.9.0 + - tbb=2021.11.0 + - tblib=3.0.0 + - tenacity=8.5.0 + - terminado=0.18.1 + - text-unidecode=1.3 + - textdistance=4.6.3 + - threadpoolctl=3.5.0 + - three-merge=0.1.1 + - tifffile=2024.7.24 + - tinycss2=1.3.0 + - tk=8.6.13 + - toml=0.10.2 + - tomli=2.0.1 + - tomlkit=0.13.0 + - toolz=0.12.1 + - torchaudio=2.0.0 + - torchvision=0.15.2 + - tornado=6.4.1 + - tqdm=4.66.4 + - traitlets=5.14.3 + - types-python-dateutil=2.9.0.20240316 + - typing-extensions=4.12.2 + - typing_extensions=4.12.2 + - tzdata=2024a + - ucx=1.14.1 + - ujson=5.10.0 + - uncertainties=3.2.2 + - unicodedata2=15.1.0 + - urllib3=2.2.2 + - watchdog=4.0.1 + - wcwidth=0.2.13 + - webencodings=0.5.1 + - websocket-client=1.8.0 + - wheel=0.43.0 + - widgetsnbextension=3.6.7 + - wurlitzer=3.1.1 + - x264=1!164.3095 + - x265=3.5 + - xarray=2024.3.0 + - xcb-util=0.4.0 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.0 + - xcb-util-renderutil=0.3.9 + - xcb-util-wm=0.4.1 + - xkeyboard-config=2.42 + - xorg-compositeproto=0.4.2 + - xorg-damageproto=1.2.1 + - xorg-fixesproto=5.0 + - xorg-inputproto=2.3.2 + - xorg-kbproto=1.0.7 + - xorg-libice=1.1.1 + - xorg-libsm=1.2.4 + - xorg-libx11=1.8.9 + - xorg-libxau=1.0.11 + - xorg-libxcomposite=0.4.6 + - xorg-libxdamage=1.1.5 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxfixes=5.0.3 + - xorg-libxi=1.7.10 + - xorg-libxrandr=1.5.2 + - xorg-libxrender=0.9.11 + - xorg-libxtst=1.2.4 + - xorg-randrproto=1.5.0 + - xorg-recordproto=1.14.2 + - xorg-renderproto=0.11.1 + - xorg-util-macros=1.19.3 + - xorg-xextproto=7.3.0 + - xorg-xf86vidmodeproto=2.3.1 + - xorg-xproto=7.0.31 + - xraylib=4.1.4 + - xyzservices=2024.6.0 + - xz=5.2.6 + - yaml=0.2.5 + - yapf=0.40.1 + - yarl=1.9.4 + - zeromq=4.3.5 + - zfp=1.0.1 + - zict=3.0.0 + - zipp=3.19.2 + - zlib=1.2.13 + - zlib-ng=2.0.7 + - zstandard=0.23.0 + - zstd=1.5.6 +prefix: /gpfs/exfel/sw/software/mambaforge/22.11/envs/202402 diff --git a/environments/202402/environment.yml b/environments/202402/environment.yml new file mode 100644 index 00000000..7c5db9cd --- /dev/null +++ b/environments/202402/environment.yml @@ -0,0 +1,107 @@ +name: "202402" +channels: + - nodefaults + - /gpfs/exfel/sw/software/euxfel-environment-management/custom-recipes/conda-bld + - conda-forge +dependencies: + - python=3.10 + - brotlipy=0.7.0 + - certipy=0.1.3 + - ipykernel=6.13.1 + - ipympl=0.9.3 + - ipython=7.33.0 + - ipython_genutils=0.2.0 + - ipywidgets=7.7.0 + - jupyter=1.0.0 + - jupyter-resource-usage=0.7.1 + - jupyter-server-mathjax=0.2.6 + - jupyter-server-proxy=4.1.0 + - jupyter_client=7.3.4 + - jupyter_console=6.4.3 + - jupyter_core=4.10.0 + - jupyter_server=1.17.1 + - jupyter_telemetry=0.1.0 + - jupyterhub=2.3.1 + - jupyterhub-base=2.3.1 + - jupyterlab=3.4.3 + - jupyterlab-git=0.41.0 + - jupyterlab-h5web=7.0.0 + - jupyterlab_code_formatter=1.6.0 + - jupyterlab_pygments=0.2.2 + - jupyterlab_server=2.14.0 + - jupyterlab_widgets=1.1.0 + - matplotlib=3.5.2 + - matplotlib-base=3.5.2 + - matplotlib-inline=0.1.3 + - pyls-spyder=0.4.0 + - scipy=1.8.1 + - spyder=5.3.1 + - spyder-kernels=2.3.1 + - astropy + - bokeh + - curl + - cython + - dask + - dask-jobqueue + - dask-labextension + - datashader + - fabio + - fast-histogram + - fftw + - h5glance>=0.8.1 + - h5netcdf + - h5py + - hvplot + - imageio + - iminuit + - jupyterlab-lsp + - kafka-python-ng + - lmfit + - mpl-interactions + - msgpack-numpy + - msgpack-python + - natsort + - netcdf4 + - numba + - numpy + - opencv + - papermill + - pint + - plotly + - polars + - pyabel + - pybaselines + - pyfai + - pyopengl + - pyqtgraph + - pytest + - python-kaleido + - pywavelets + - pyzmq<25 + - scikit-beam + - scikit-image + - scikit-learn + - seaborn + - silx + - xarray + - xraylib + - calibration-client >=11.3.0 + - cfelpyutils + - condat-gridconv + - damnit + - envmodules + - euxfel-bunch-pattern + - extra-data >= 1.14 + - extra-geom + - extra-hed + - findxfel + - hdf5-vds-check + - karabo-bridge + - karabo_bridge_recorder + - matplotlib-scalebar + - metadata-client + - metropc + - nbclick + - pasha + - princess + - condor diff --git a/modules/exfel-python/202402 b/modules/exfel-python/202402 new file mode 100644 index 00000000..67666a98 --- /dev/null +++ b/modules/exfel-python/202402 @@ -0,0 +1,22 @@ +#%Module 1.0 +proc ModulesHelp {} { + puts stdout "Mamba environment for cycle 202402" +} + +module-whatis "Module loads the mamba environment for cycle 202402" + +if { [ module-info mode load ] } { + system "/gpfs/exfel/sw/software/local/etc/metrics.sh 'mamba/202402'" +} + +module load mambaforge + +prepend-path PATH /gpfs/exfel/sw/software/mambaforge/22.11/envs/202402/bin +prepend-path XML_CATALOG_FILES file {///gpfs/exfel/sw/software/mambaforge/22.11/envs/202402/etc/xml/catalog file} ///etc/xml/catalog +setenv CONDA_DEFAULT_ENV 202402 +setenv CONDA_PREFIX /gpfs/exfel/sw/software/mambaforge/22.11/envs/202402 +setenv CONDA_PROMPT_MODIFIER {(202402) } +setenv CONDA_SHLVL 1 +setenv GSETTINGS_SCHEMA_DIR /gpfs/exfel/sw/software/mambaforge/22.11/envs/202402/share/glib-2.0/schemas +setenv GSETTINGS_SCHEMA_DIR_CONDA_BACKUP {} + From 948f3c88e2df16644ae4e4e0f59f746ae9e3cb9d Mon Sep 17 00:00:00 2001 From: James Wrigley Date: Thu, 1 Aug 2024 15:01:25 +0200 Subject: [PATCH 6/6] Updated the default module --- modules/exfel-python/.version | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/exfel-python/.version b/modules/exfel-python/.version index c7c104e4..ce4817e4 100644 --- a/modules/exfel-python/.version +++ b/modules/exfel-python/.version @@ -1,3 +1,3 @@ #%Module1.0 # Set default version -set ModulesVersion "202401" +set ModulesVersion "202402"