Merge pull request #346 from ZLLentz/rel-5.9.1

pcds-5.9.1

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
@@ -37,28 +37,27 @@ 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
 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
 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

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
@@ -73,21 +73,21 @@ 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
   - brunsli=0.1=h9c3ff4c_0
   - 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

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

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