diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index 9c1b853..f5e2ed2 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -3,8 +3,8 @@ ads-async>=0.3.1 anaconda-client>=1.12.3 apischema>=0.18.0 archapp>=1.1.0 -atef>=1.5.0 -atlassian-python-api>=3.41.14 +atef>=1.5.1 +atlassian-python-api>=3.41.16 black>=24.8.0 blark>=0.8.1 bluesky-live>=0.0.8 @@ -14,7 +14,7 @@ botorch>=0.4.0 caproto>=1.1.1 coloredlogs>=15.0.1 conda-pack>=0.8.0 -conda-smithy>=3.39.0 +conda-smithy>=3.40.1 cookiecutter>=2.1.1 coverage>=7.6.1 cython>=0.29.34 @@ -23,10 +23,10 @@ elog>=1.2.3 epicsmacrolib>=0.6.1 flake8>=7.1.1 flask>=3.0.3 -fzf>=0.54.3 +fzf>=0.55.0 gdb>=15.1 -gh>=2.55.0 -ghapi>=1.0.5 +gh>=2.57.0 +ghapi>=1.0.6 gpytorch>=1.4.2 h5py>=3.3.0 happi>=2.5.0 @@ -37,8 +37,7 @@ 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 +lightpath>=1.0.5 lucid>=0.11.0 lxml>=4.8.0 memray>=1.13.4 @@ -46,7 +45,7 @@ mysqlclient>=2.0.3 nabs>=1.5.5 numpy>=1.14,<2.0.0 opencv>=4.5.1[build='^qt5.*$'] -openssl>=3.3.1 +openssl>=3.3.2 pandas>=1.5.3 panel>=0.14.4 papermill>=2.3.4 @@ -54,11 +53,11 @@ paramiko>=3.1.0 pcaspy>=0.7.3 pcdscalc>=0.6.0 pcdsdaq>=2.4.4 -pcdsdevices>=8.5.0 +pcdsdevices>=8.6.0 pcdsutils>=0.14.1 pcdswidgets>=0.8.3 periodictable>=1.5.2 -pipdeptree>=2.23.1 +pipdeptree>=2.23.4 pmgr>=2.1.3 pmpsdb_client>=1.2.0 pre-commit>=3.8.0 @@ -74,11 +73,11 @@ pyfiglet>=0.8 pymongo>=4.3.3 py-spy>=0.3.14 pytables>=3.6.1 -pytest>=8.3.2 +pytest>=8.3.3 pytest-qt>=4.4.0 pytest-repeat>=0.9.2 pytest-xdist>=3.6.1 -pytmc>=2.16.0 +pytmc>=2.17.0 pytorch>=2.0.0 pyupgrade>=3.17.0 pyyaml>=6.0 @@ -110,6 +109,7 @@ typhos>=4.0.0 whatrecord>=0.6.0 xarray>=2023.3.0 xraylib>=4.1.3 +xopt>=2.3.0 yarn>=3.5.0 # conda only regressive pins # pin for gui interface stability @@ -122,6 +122,8 @@ bluesky-base=1.10.0 databroker=1.2.5 # ipython changes make scientists upset and can break experiments ipython=8.4.0 +# newer line_profiler requires newer ipython +line_profiler=4.1.1 # 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 diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index 6cefdb0..02847d1 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -1,4 +1,4 @@ -name: pcds-5.9.0 +name: pcds-5.9.1 channels: - conda-forge - pcds-tag @@ -29,9 +29,9 @@ dependencies: - astunparse=1.6.3=pyhd8ed1ab_0 - async-lru=2.0.4=pyhd8ed1ab_0 - async-timeout=4.0.3=pyhd8ed1ab_0 - - atef=1.5.0=pyhd8ed1ab_0 + - atef=1.5.1=pyhd8ed1ab_0 - atk-1.0=2.38.0=h04ea711_2 - - atlassian-python-api=3.41.14=pyhd8ed1ab_0 + - atlassian-python-api=3.41.16=pyhd8ed1ab_0 - attr=2.5.1=h166bdaf_1 - attrs=24.2.0=pyh71513ae_0 - aws-c-auth=0.7.26=hc36b679_2 @@ -73,7 +73,7 @@ dependencies: - bokeh=3.4.2=pyhd8ed1ab_0 - boltons=24.0.0=pyhd8ed1ab_0 - boolean.py=4.0=pyhd8ed1ab_0 - - botorch=0.11.3=pyhd8ed1ab_0 + - botorch=0.10.0=pyhd8ed1ab_0 - brotli=1.1.0=hd590300_1 - brotli-bin=1.1.0=hd590300_1 - brotli-python=1.1.0=py39h3d6467e_1 @@ -81,13 +81,13 @@ dependencies: - bzip2=1.0.8=h4bc722e_7 - c-ares=1.32.3=h4bc722e_0 - c-blosc2=2.15.1=hc57e6cf_0 - - ca-certificates=2024.7.4=hbcca054_0 + - ca-certificates=2024.8.30=hbcca054_0 - cached-property=1.5.2=hd8ed1ab_1 - cached_property=1.5.2=pyha770c72_1 - cachetools=5.5.0=pyhd8ed1ab_0 - cairo=1.18.0=hbb29018_2 - caproto=1.1.1=pyhd8ed1ab_0 - - certifi=2024.7.4=pyhd8ed1ab_0 + - certifi=2024.8.30=pyhd8ed1ab_0 - cffi=1.17.0=py39h49a4b6b_0 - cfgv=3.3.1=pyhd8ed1ab_0 - chardet=5.2.0=py39hf3d152e_1 @@ -110,12 +110,12 @@ dependencies: - conda-pack=0.8.0=pyhd8ed1ab_0 - conda-package-handling=2.3.0=pyh7900ff3_0 - conda-package-streaming=0.10.0=pyhd8ed1ab_0 - - conda-smithy=3.39.0=unix_pyh707e725_0 + - conda-smithy=3.40.1=unix_pyh707e725_0 - contextlib2=21.6.0=pyhd8ed1ab_0 - contourpy=1.2.1=py39h7633fee_0 - cookiecutter=2.6.0=pyhca7485f_0 - coverage=7.6.1=py39hcd6043d_0 - - cryptography=43.0.0=py39h5c34e2d_0 + - cryptography=43.0.1=py39h7170ec2_0 - curio=1.4=py_0 - cycler=0.12.1=pyhd8ed1ab_0 - cyrus-sasl=2.1.27=h54b06d7_7 @@ -128,6 +128,7 @@ dependencies: - datashader=0.16.3=pyhd8ed1ab_0 - dav1d=1.2.1=hd590300_0 - dbus=1.13.6=h5008d03_3 + - deap=1.4.1=py39h3b40f6f_3 - debugpy=1.8.5=py39h98e3656_0 - decorator=5.1.1=pyhd8ed1ab_0 - defusedxml=0.7.1=pyhd8ed1ab_0 @@ -159,7 +160,7 @@ dependencies: - executing=2.0.1=pyhd8ed1ab_0 - expat=2.6.2=h59595ed_0 - fabric=3.2.2=pyhd8ed1ab_0 - - fastcore=1.7.1=pyhd8ed1ab_0 + - fastcore=1.7.8=pyhd8ed1ab_0 - fasteners=0.17.3=pyhd8ed1ab_0 - ffmpeg=6.1.2=gpl_h226ea3b_102 - filelock=3.15.4=pyhd8ed1ab_0 @@ -186,7 +187,7 @@ dependencies: - fsspec=2024.6.1=pyhff2d567_0 - future=1.0.0=pyhd8ed1ab_0 - fuzzywuzzy=0.18.0=pyhd8ed1ab_0 - - fzf=0.54.3=ha8f183a_0 + - fzf=0.55.0=ha8f183a_0 - g-ir-build-tools=1.80.1=py39h673cbd7_0 - g-ir-host-tools=1.80.1=hfff48b1_0 - gdb=15.1=py39h4909cf3_0 @@ -195,8 +196,8 @@ dependencies: - gettext=0.22.5=he02047a_3 - gettext-tools=0.22.5=he02047a_3 - gflags=2.2.2=he1b5a44_1004 - - gh=2.55.0=h76a2195_0 - - ghapi=1.0.5=pyhd8ed1ab_0 + - gh=2.57.0=h76a2195_0 + - ghapi=1.0.6=pyhd8ed1ab_0 - ghp-import=2.1.0=pyhd8ed1ab_0 - giflib=5.2.2=hd590300_0 - git=2.46.0=pl5321hb5640b7_0 @@ -209,7 +210,7 @@ dependencies: - gmpy2=2.1.5=py39h048c657_1 - gnutls=3.8.7=h32866dd_0 - gobject-introspection=1.80.1=py39hb25b1be_0 - - gpytorch=1.12=pyhd8ed1ab_0 + - gpytorch=1.11=pyhd8ed1ab_0 - graphite2=1.3.13=h59595ed_1003 - graphviz=12.0.0=hba01fac_0 - greenlet=3.0.3=py39h3d6467e_0 @@ -317,12 +318,12 @@ dependencies: - libasprintf-devel=0.22.5=he8f35ee_3 - libass=0.17.3=h1dc1e6a_0 - libavif16=1.1.1=h104a339_1 - - libblas=3.9.0=23_linux64_openblas + - libblas=3.9.0=20_linux64_mkl - libbrotlicommon=1.1.0=hd590300_1 - libbrotlidec=1.1.0=hd590300_1 - libbrotlienc=1.1.0=hd590300_1 - libcap=2.69=h0f662aa_0 - - libcblas=3.9.0=23_linux64_openblas + - libcblas=3.9.0=20_linux64_mkl - libclang-cpp15=15.0.7=default_h127d8a8_5 - libclang13=18.1.8=default_h9def88c_2 - libcrc32c=1.1.2=h9c3ff4c_0 @@ -338,7 +339,8 @@ dependencies: - libexpat=2.6.2=h59595ed_0 - libffi=3.4.2=h7f98852_5 - libflac=1.4.3=h59595ed_0 - - libgcc-ng=14.1.0=h77fa898_0 + - libgcc=14.1.0=h77fa898_1 + - libgcc-ng=14.1.0=h69a702a_1 - libgcrypt=1.11.0=h4ab18f5_1 - libgd=2.3.3=h119a65a_9 - libgettextpo=0.22.5=he02047a_3 @@ -358,8 +360,8 @@ dependencies: - libidn2=2.3.7=hd590300_0 - libjpeg-turbo=3.0.0=hd590300_1 - libjxl=0.10.3=h66b40c8_0 - - liblapack=3.9.0=23_linux64_openblas - - liblapacke=3.9.0=23_linux64_openblas + - liblapack=3.9.0=20_linux64_mkl + - liblapacke=3.9.0=20_linux64_mkl - liblief=0.14.1=hac33072_1 - libllvm14=14.0.6=hcd5def8_4 - libllvm15=15.0.7=hb3ce162_4 @@ -400,7 +402,8 @@ dependencies: - libsolv=0.7.30=h3509ff9_0 - libsqlite=3.46.0=hde9e2c9_0 - libssh2=1.11.0=h0841786_0 - - libstdcxx-ng=14.1.0=hc0a3c3a_0 + - libstdcxx=14.1.0=hc0a3c3a_1 + - libstdcxx-ng=14.1.0=h4852527_1 - libsystemd0=255=h3516f8a_1 - libtasn1=4.19.0=h166bdaf_0 - libthrift=0.20.0=h0e7cc3e_1 @@ -424,9 +427,10 @@ dependencies: - libzlib=1.3.1=h4ab18f5_1 - libzopfli=1.0.3=h9c3ff4c_0 - license-expression=30.1.1=pyhd8ed1ab_0 - - lightpath=1.0.4=pyhd8ed1ab_0 + - lightpath=1.0.5=pyhd8ed1ab_0 + - lightpath-base=1.0.5=pyhd8ed1ab_0 - line_profiler=4.1.1=py39h7633fee_1 - - linear_operator=0.5.2=pyhd8ed1ab_0 + - linear_operator=0.5.1=pyhd8ed1ab_0 - linkify-it-py=2.0.3=pyhd8ed1ab_0 - llvm-openmp=18.1.8=hf5423f3_1 - llvmlite=0.43.0=py39h81bab63_0 @@ -488,13 +492,13 @@ dependencies: - networkx=3.2.1=pyhd8ed1ab_0 - nodeenv=1.9.1=pyhd8ed1ab_0 - nodejs=22.6.0=h6d9b948_0 - - notebook=7.2.1=pyhd8ed1ab_0 + - notebook=7.2.2=pyhd8ed1ab_0 - notebook-shim=0.2.4=pyhd8ed1ab_0 - nspr=4.35=h27087fc_0 - nss=3.103=h593d115_0 - numba=0.60.0=py39h0320e7d_0 - numcodecs=0.12.1=py39h84cc369_1 - - numexpr=2.7.3=py39hde0f152_1 + - numexpr=2.10.0=mkl_py39h260461e_0 - numpy=1.26.4=py39h474f0d3_0 - numpydoc=1.8.0=pyhd8ed1ab_0 - oauthlib=3.2.2=pyhd8ed1ab_0 @@ -504,10 +508,11 @@ dependencies: - openh264=2.4.1=h59595ed_0 - openjpeg=2.5.2=h488ebb8_0 - openpyxl=3.1.5=py39hd1e30aa_0 - - openssl=3.3.1=hb9d3cd8_3 + - openssl=3.3.2=hb9d3cd8_0 - ophyd=1.7.0=pyhd8ed1ab_0 - opt_einsum=3.3.0=pyhc1e730c_2 - orc=2.0.2=h669347b_0 + - orjson=3.10.7=py39h5cde264_0 - outcome=1.3.0.post0=pyhd8ed1ab_0 - overrides=7.7.0=pyhd8ed1ab_0 - p11-kit=0.24.1=hc5aa10d_0 @@ -530,7 +535,7 @@ dependencies: - pcaspy=0.8.1=py39hddac248_0 - pcdscalc=0.6.0=pyhd8ed1ab_0 - pcdsdaq=2.4.4=py_0 - - pcdsdevices=8.5.0=pyhd8ed1ab_0 + - pcdsdevices=8.6.0=pyhd8ed1ab_0 - pcdsutils=0.14.1=pyhd8ed1ab_1 - pcdswidgets=0.8.3=pyhd8ed1ab_0 - pcre2=10.44=hba22ea6_2 @@ -542,7 +547,7 @@ dependencies: - pims=0.7=pyhd8ed1ab_0 - pint=0.24.3=pyhd8ed1ab_0 - pip=24.2=pyhd8ed1ab_0 - - pipdeptree=2.23.1=pyhd8ed1ab_0 + - pipdeptree=2.23.4=pyhd8ed1ab_0 - pixman=0.43.2=h59595ed_0 - pkg-config=0.29.2=h4bc722e_1009 - pkginfo=1.11.1=pyhd8ed1ab_0 @@ -613,7 +618,7 @@ dependencies: - pysocks=1.7.1=pyha2e5f31_6 - pyspnego=0.11.1=py39hf3d152e_0 - pytables=3.9.2=py39hd89fbf8_3 - - pytest=8.3.2=pyhd8ed1ab_0 + - pytest=8.3.3=pyhd8ed1ab_0 - pytest-asyncio=0.24.0=pyhd8ed1ab_0 - pytest-benchmark=4.0.0=pyhd8ed1ab_0 - pytest-cov=5.0.0=pyhd8ed1ab_0 @@ -635,7 +640,7 @@ dependencies: - python-tzdata=2024.1=pyhd8ed1ab_0 - python_abi=3.9=5_cp39 - pytkdocs=0.16.1=pyhd8ed1ab_1 - - pytmc=2.16.0=pyhd8ed1ab_0 + - pytmc=2.17.0=pyhd8ed1ab_0 - pytorch=2.4.0=cpu_mkl_py39h85c4de8_100 - pytz=2024.1=pyhd8ed1ab_0 - pyupgrade=3.17.0=pyhd8ed1ab_0 @@ -805,6 +810,7 @@ dependencies: - xcb-util-renderutil=0.3.10=hb711507_0 - xcb-util-wm=0.4.2=hb711507_0 - xkeyboard-config=2.42=h4ab18f5_0 + - xopt=2.3.0=pyhd8ed1ab_1 - xorg-compositeproto=0.4.2=h7f98852_1001 - xorg-damageproto=1.2.1=h7f98852_1002 - xorg-fixesproto=5.0=h7f98852_1002 @@ -878,4 +884,4 @@ dependencies: - python-vxi11==0.9 - slac-alarm-manager==1.3.0 - tc-release==0.2.6 -prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-5.9.0 +prefix: /home/runner/miniconda/envs/pcds-5.9.1 diff --git a/envs/pcds/keep-updated.txt b/envs/pcds/keep-updated.txt index f1fa79e..bd549d3 100644 --- a/envs/pcds/keep-updated.txt +++ b/envs/pcds/keep-updated.txt @@ -46,6 +46,7 @@ caproto hklpy # ophyd (need to test v1.8.0) pyepics +xopt # Developer tools # - General tools for Python developers @@ -66,7 +67,7 @@ gh ghapi grpcio-tools isort -line_profiler +# line_profiler (locked with ipython) memray pipdeptree pre-commit diff --git a/envs/pcds/security-packages.txt b/envs/pcds/security-packages.txt index 8e42bd6..6983502 100644 --- a/envs/pcds/security-packages.txt +++ b/envs/pcds/security-packages.txt @@ -1,4 +1,6 @@ # Extra dependencies that must be updated to handle a CVE # Apply this even in the incr environment # This file can be periodically cleared after an env release -aiohttp>=3.10.2 +cryptography>=43.0.1 +notebook>=7.2.2 +numexpr>=2.8.4