From 0a960c6f6223d9f285bb1ac4460a526dbfcf9929 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 10:47:42 -0700 Subject: [PATCH 01/11] ENH: updated pcds to 4.1.0 --- envs/pcds/env.yaml | 202 ++++++++++++++++++++++++++------------------- 1 file changed, 115 insertions(+), 87 deletions(-) diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index 1504c001..beb01ed1 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -1,19 +1,22 @@ -name: pcds-4.0.1 +name: pcds-4.1.0 channels: - conda-forge - pcds-tag + - lcls-ii dependencies: - _libgcc_mutex=0.1 - _openmp_mutex=4.5 - - ads-async=0.0.2 + - abseil-cpp=20200923.3 + - ads-async=0.1.0 - alabaster=0.7.12 - alsa-lib=1.2.3 + - amityping=1.1.6 - anaconda-client=1.7.2 - ansiwrap=0.8.4 - appdirs=1.4.4 - archapp=1.0.0 - argon2-cffi=20.1.0 - - arrow=1.0.2 + - arrow=1.0.3 - asciitree=0.3.3 - asteval=0.9.23 - async_generator=1.10 @@ -22,7 +25,7 @@ dependencies: - babel=2.9.0 - backcall=0.2.0 - backports=1.0 - - backports.functools_lru_cache=1.6.1 + - backports.functools_lru_cache=1.6.3 - beautifulsoup4=4.9.3 - binaryornot=0.4.4 - black=20.8b1 @@ -34,16 +37,18 @@ dependencies: - bokeh=2.3.0 - boltons=20.2.1 - boolean.py=3.7 + - boost-cpp=1.74.0 - brotli=1.0.9 - brotlipy=0.7.0 - brunsli=0.1 - bzip2=1.0.8 - c-ares=1.17.1 - ca-certificates=2020.12.5 - - cached-property=1.5.1 + - cached-property=1.5.2 + - cached_property=1.5.2 - cachetools=4.2.1 - cairo=1.16.0 - - caproto=0.7.1 + - caproto=0.8.0 - certifi=2020.12.5 - cffi=1.14.5 - cfgv=3.2.0 @@ -57,30 +62,32 @@ dependencies: - coloredlogs=15.0 - conda=4.9.2 - conda-build=3.21.4 - - conda-forge-pinning=2021.03.03.20.57.29 + - conda-forge-pinning=2021.03.29.15.45.30 - conda-pack=0.6.0 - conda-package-handling=1.7.2 - conda-smithy=3.9.0 - contextlib2=0.5.5 - cookiecutter=1.7.2 - coverage=5.5 - - cryptography=3.4.4 + - cryptography=3.4.7 - curio=1.4 - - curl=7.71.1 + - curl=7.75.0 - cycler=0.10.0 + - cyrus-sasl=2.1.27 + - cython=0.29.22 - cytoolz=0.11.0 - - dask=2021.2.0 - - dask-core=2021.2.0 - - databroker=1.2.2 - - dataclasses=0.7 - - datashader=0.12.0 + - dask=2021.3.1 + - dask-core=2021.3.1 + - databroker=1.2.3 + - dataclasses=0.8 + - datashader=0.12.1 - datashape=0.5.4 - dbus=1.13.6 - decorator=4.4.2 - - defusedxml=0.6.0 + - defusedxml=0.7.1 - deprecated=1.2.10 - distlib=0.3.1 - - distributed=2021.2.0 + - distributed=2021.3.1 - docopt=0.6.2 - doct=1.1.0 - doctr=1.8.0 @@ -89,16 +96,16 @@ dependencies: - editdistance=0.5.3 - elog=1.0.2 - entrypoints=0.3 - - epics-base=7.0.4 + - epics-base=7.0.5.0 - epics-pypdb=0.1.5 - epicscorelibs=7.0.3.99.4.0 - et_xmlfile=1.0.1 - event-model=1.17.1 - - expat=2.2.10 + - expat=2.3.0 - fasteners=0.14.1 - ffmpeg=4.3.1 - filelock=3.0.12 - - flake8=3.8.4 + - flake8=3.9.0 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=2.001 - font-ttf-source-code-pro=2.030 @@ -111,56 +118,57 @@ dependencies: - fsspec=0.8.7 - future=0.18.2 - fuzzywuzzy=0.18.0 - - fzf=0.25.1 - - gdk-pixbuf=2.42.2 + - fzf=0.26.0 + - gdk-pixbuf=2.42.4 - gettext=0.19.8.1 - gh=1.6.2 - giflib=5.2.1 - - git=2.30.1 - - gitdb=4.0.5 + - git=2.30.2 + - gitdb=4.0.7 - gitpython=3.1.14 - - glib=2.66.7 - - glib-tools=2.66.7 + - glib=2.68.0 + - glib-tools=2.68.0 - glob2=0.7 - gmp=6.2.1 - gnutls=3.6.13 - graphite2=1.3.13 - - graphviz=2.46.1 + - graphviz=2.47.0 + - greenlet=1.0.0 - grpcio=1.33.2 - grpcio-tools=1.33.2 - gst-plugins-base=1.14.5 - - gstreamer=1.18.3 + - gstreamer=1.18.4 - gtk2=2.24.33 - gts=0.7.6 - h5py=3.1.0 - happi=1.9.0 - - harfbuzz=2.7.4 + - harfbuzz=2.8.0 - hdf5=1.10.6 - heapdict=1.0.1 - helpdev=0.7.1 - historydict=1.2.3 - holoviews=1.14.2 - humanfriendly=9.1 - - humanize=3.2.0 + - humanize=3.3.0 - hutch-python=1.9.1 - hxrsnd=0.2.4 - icu=68.1 - - identify=2.1.0 + - identify=2.1.4 - idna=2.10 - imagecodecs=2021.1.28 - imageio=2.9.0 - imagesize=1.2.0 - - importlib-metadata=3.7.0 - - importlib_metadata=3.7.0 - - importlib_resources=5.1.1 + - importlib-metadata=3.10.0 + - importlib_metadata=3.10.0 + - importlib_resources=5.1.2 - iniconfig=1.1.1 - - intake=0.6.1 - - ipykernel=5.5.0 - - ipython=7.21.0 + - intake=0.6.2 + - ipykernel=5.5.3 + - ipython=7.22.0 - ipython_genutils=0.2.0 - ipywidgets=7.6.3 - isodate=0.6.0 - - isort=5.7.0 + - isort=5.8.0 - jack=0.125.0 - jasper=1.900.1 - jdcal=1.4.1 @@ -171,8 +179,8 @@ dependencies: - jpeg=9d - jsonschema=3.2.0 - jupyter=1.0.0 - - jupyter_client=6.1.11 - - jupyter_console=6.2.0 + - jupyter_client=6.1.12 + - jupyter_console=6.4.0 - jupyter_core=4.7.1 - jupyterlab_pygments=0.1.2 - jupyterlab_widgets=1.0.0 @@ -188,8 +196,8 @@ dependencies: - libarchive=3.5.1 - libblas=3.9.0 - libcblas=3.9.0 - - libclang=11.0.1 - - libcurl=7.71.1 + - libclang=11.1.0 + - libcurl=7.75.0 - libdb=6.2.32 - libdeflate=1.7 - libedit=3.1.20191231 @@ -197,23 +205,24 @@ dependencies: - libevent=2.1.10 - libffi=3.3 - libgcc-ng=9.3.0 - - libgd=2.3.0 + - libgd=2.3.2 - libgfortran-ng=9.3.0 - libgfortran5=9.3.0 - - libglib=2.66.7 + - libglib=2.68.0 - libgomp=9.3.0 - libiconv=1.16 - liblapack=3.9.0 - liblapacke=3.9.0 - liblief=0.10.1 - libllvm10=10.0.1 - - libllvm11=11.0.1 + - libllvm11=11.1.0 - libnghttp2=1.43.0 + - libntlm=1.4 - libopenblas=0.3.12 - libopencv=4.5.1 - libpng=1.6.37 - libpq=12.3 - - libprotobuf=3.15.3 + - libprotobuf=3.15.6 - librsvg=2.50.3 - libsodium=1.0.18 - libssh2=1.9.0 @@ -232,11 +241,11 @@ dependencies: - license-expression=1.2 - lightpath=0.6.8 - line_profiler=3.1.0 - - llvmlite=0.35.0 + - llvmlite=0.36.0 - lmfit=1.0.2 - locket=0.2.0 - lucid=0.7.2 - - lxml=4.6.2 + - lxml=4.6.3 - lz4-c=1.9.3 - lzo=2.10 - markdown=3.3.4 @@ -246,9 +255,13 @@ dependencies: - mccabe=0.6.1 - mistune=0.8.4 - mock=4.0.3 + - mongodb=4.2.13 - mongoquery=1.3.5 - monotonic=1.5 - more-itertools=8.7.0 + - mpi=1.0 + - mpi4py=3.0.3 + - mpich=3.4.1 - msgpack-numpy=0.4.7.1 - msgpack-python=1.0.2 - msrest=0.6.21 @@ -267,30 +280,33 @@ dependencies: - nettle=3.6 - networkx=2.5 - nodeenv=1.5.0 - - notebook=6.2.0 - - nspr=4.29 - - nss=3.62 - - numba=0.52.0 + - nose=1.3.7 + - notebook=6.3.0 + - nspr=4.30 + - nss=3.63 + - numba=0.53.1 - numcodecs=0.7.3 - - numexpr=2.7.2 - - numpy=1.20.1 + - numexpr=2.7.3 + - numpy=1.20.2 - numpydoc=1.1.0 - oauthlib=3.0.1 - olefile=0.46 - opencv=4.5.1 - openh264=2.1.1 - openjpeg=2.4.0 - - openpyxl=3.0.6 - - openssl=1.1.1j + - openldap=2.4.52 + - openpyxl=3.0.7 + - openssl=1.1.1k - ophyd=1.6.1 - outcome=1.1.0 + - p4p=3.5.2 - packaging=20.9 - pandas=1.2.3 - - pandoc=2.11.4 + - pandoc=2.12 - pandocfilters=1.4.2 - - panel=0.11.0 + - panel=0.11.1 - pango=1.42.4 - - papermill=2.3.2 + - papermill=2.3.3 - param=1.10.1 - parso=0.8.1 - partd=1.1.0 @@ -308,9 +324,9 @@ dependencies: - perl=5.32.0 - pexpect=4.8.0 - pickleshare=0.7.5 - - pillow=8.1.1 + - pillow=8.1.2 - pims=0.5 - - pint=0.16.1 + - pint=0.17 - pip=21.0.1 - pixman=0.40.0 - pkginfo=1.7.0 @@ -320,13 +336,17 @@ dependencies: - pooch=1.3.0 - portaudio=19.6.0 - poyo=0.5.0 - - pre-commit=2.10.1 + - pre-commit=2.11.1 - prettytable=2.1.0 - prometheus_client=0.9.0 - - prompt-toolkit=3.0.16 - - prompt_toolkit=3.0.16 - - protobuf=3.15.3 + - prompt-toolkit=3.0.18 + - prompt_toolkit=3.0.18 + - protobuf=3.15.6 + - psalg=3.3.14 + - psana=3.3.14 + - psdaq-control-minimal=3.3.14 - psdm_qs_cli=0.3.1 + - psmon=1.0.2 - psutil=5.8.0 - pswalker=1.0.6 - pthread-stubs=0.4 @@ -336,20 +356,23 @@ dependencies: - py-lief=0.10.1 - py-opencv=4.5.1 - py-spy=0.3.4 + - pyabel=0.8.3 + - pyasn1=0.4.8 + - pyasn1-modules=0.2.7 - pyaudio=0.2.11 - pyca=3.1.1 - - pycodestyle=2.6.0 + - pycodestyle=2.7.0 - pycosat=0.6.3 - pycparser=2.20 - pycrypto=2.6.1 - pyct=0.4.6 - pyct-core=0.4.6 - - pydm=1.10.7 + - pydm=1.11.0 - pyepics=3.4.3 - pyfiglet=0.8.post1 - - pyflakes=2.2.0 + - pyflakes=2.3.1 - pygithub=1.53 - - pygments=2.8.0 + - pygments=2.8.1 - pyjwt=2.0.1 - pykerberos=1.2.1 - pymongo=3.11.0 @@ -361,7 +384,7 @@ dependencies: - pyqt5-sip=4.19.18 - pyqtads=3.7.0 - pyqtchart=5.12 - - pyqtgraph=0.11.1 + - pyqtgraph=0.12.0 - pyqtwebengine=5.12.1 - pyrsistent=0.17.3 - pysocks=1.7.1 @@ -373,6 +396,7 @@ dependencies: - python=3.8.8 - python-dateutil=2.8.1 - python-graphviz=0.16 + - python-ldap=3.3.1 - python-levenshtein=0.12.2 - python-libarchive-c=2.9 - python-slugify=4.0.1 @@ -386,21 +410,22 @@ dependencies: - qdarkstyle=2.8.1 - qt=5.12.9 - qtawesome=1.0.2 - - qtconsole=5.0.2 + - qtconsole=5.0.3 - qtpy=1.9.0 - qtpyinheritance=0.0.1 - readline=8.0 - - regex=2020.11.13 + - regex=2021.3.17 - requests=2.25.1 - requests-oauthlib=1.3.0 - ripgrep=12.1.1 + - roentdek=0.0.3 - ruamel.yaml=0.16.12 - ruamel.yaml.clib=0.2.2 - ruamel_yaml=0.15.80 - schema=0.7.4 - scikit-image=0.18.1 - scikit-learn=0.24.1 - - scipy=1.6.0 + - scipy=1.6.2 - scrypt=0.8.17 - seaborn=0.11.1 - seaborn-base=0.11.1 @@ -416,7 +441,7 @@ dependencies: - snowballstemmer=2.1.0 - sortedcontainers=2.3.0 - soupsieve=2.0.1 - - sphinx=3.5.1 + - sphinx=3.5.3 - sphinx_rtd_theme=0.5.1 - sphinxcontrib-applehelp=1.0.2 - sphinxcontrib-devhelp=1.0.2 @@ -424,30 +449,31 @@ dependencies: - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.4 - - sqlalchemy=1.3.23 - - sqlite=3.34.0 + - sqlalchemy=1.4.3 + - sqlite=3.35.3 - statsmodels=0.12.2 - suitcase-mongo=0.2.0 - suitcase-msgpack=0.2.4 - suitcase-utils=0.5.3 - super_state_machine=2.0.2 - - tblib=1.6.0 + - tblib=1.7.0 - tc_release=0.2.1 - tenacity=7.0.0 - - terminado=0.9.2 + - terminado=0.9.4 - testpath=0.4.4 - text-unidecode=1.3 - textwrap3=0.9.2 - threadpoolctl=2.1.0 - - tifffile=2021.2.26 + - tifffile=2021.3.17 - timechart=1.2.3 - tk=8.6.10 - toml=0.10.2 - toolz=0.11.1 - tornado=6.1 - - tqdm=4.58.0 + - tqdm=4.59.0 - traitlets=5.0.5 - - transfocate=0.3.4 + - transfocate=0.4.0 + - transitions=0.8.7 - trio=0.18.0 - typed-ast=1.4.2 - typhos=1.1.4 @@ -455,9 +481,9 @@ dependencies: - tzlocal=2.1 - uncertainties=3.1.5 - unidecode=1.2.0 - - urllib3=1.26.3 + - urllib3=1.26.4 - versioneer=0.19 - - virtualenv=20.4.2 + - virtualenv=20.4.3 - vsts-python-api=0.1.22 - wcwidth=0.2.5 - webencodings=0.5.1 @@ -470,7 +496,7 @@ dependencies: - xorg-kbproto=1.0.7 - xorg-libice=1.0.10 - xorg-libsm=1.2.3 - - xorg-libx11=1.6.12 + - xorg-libx11=1.7.0 - xorg-libxau=1.0.9 - xorg-libxdmcp=1.1.3 - xorg-libxext=1.3.4 @@ -480,13 +506,15 @@ dependencies: - xorg-xproto=7.0.31 - xraydb=4.4.5 - xraylib=4.0.0 + - xtcdata=3.3.14 - xz=5.2.5 - yaml=0.2.5 - - zarr=2.6.1 + - yaml-cpp=0.6.3 + - zarr=2.7.0 - zeromq=4.3.4 - zfp=0.5.5 - zict=2.0.0 - - zipp=3.4.0 + - zipp=3.4.1 - zlib=1.2.11 - - zstd=1.4.8 -prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-4.0.1 + - zstd=1.4.9 +prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-4.1.0 From 970300d9d55499d1937df8b64c88404d6c84f8cd Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 11:05:04 -0700 Subject: [PATCH 02/11] ENH: updated pcds to 4.1.0 --- envs/pcds/conda-packages.txt | 10 +++++----- envs/pcds/env.yaml | 21 ++++++++++----------- 2 files changed, 15 insertions(+), 16 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index c10b570e..e7d81327 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -1,15 +1,15 @@ -ads-async>=0.0.2 +ads-async>=0.1.0 anaconda-client bluesky>=1.6.7 bluesky-live bokeh>=1.0.1 -caproto>=0.7.1 +caproto>=0.8.0 coloredlogs conda-pack conda-smithy cookiecutter coverage -databroker>=1.2.2 +databroker>=1.2.3 datashader doctr elog>=1.0.2 @@ -52,7 +52,7 @@ psdm_qs_cli>=0.3.1 pswalker>=1.0.6 pyaudio pyca>=3.1.1 -pydm>=1.10.7 +pydm>=1.11.0 pyepics>=3.4.3 pyfiglet pymongo @@ -76,7 +76,7 @@ sphinx sphinx_rtd_theme tc_release>=0.2.1 timechart>=1.2.3 -transfocate>=0.3.4 +transfocate>=0.4.0 typhos>=1.1.4 versioneer xarray diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index beb01ed1..c200046d 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -60,9 +60,9 @@ dependencies: - colorama=0.4.4 - colorcet=2.0.6 - coloredlogs=15.0 - - conda=4.9.2 + - conda=4.10.0 - conda-build=3.21.4 - - conda-forge-pinning=2021.03.29.15.45.30 + - conda-forge-pinning=2021.04.02.15.43.00 - conda-pack=0.6.0 - conda-package-handling=1.7.2 - conda-smithy=3.9.0 @@ -71,7 +71,7 @@ dependencies: - coverage=5.5 - cryptography=3.4.7 - curio=1.4 - - curl=7.75.0 + - curl=7.76.0 - cycler=0.10.0 - cyrus-sasl=2.1.27 - cython=0.29.22 @@ -145,7 +145,6 @@ dependencies: - harfbuzz=2.8.0 - hdf5=1.10.6 - heapdict=1.0.1 - - helpdev=0.7.1 - historydict=1.2.3 - holoviews=1.14.2 - humanfriendly=9.1 @@ -197,7 +196,7 @@ dependencies: - libblas=3.9.0 - libcblas=3.9.0 - libclang=11.1.0 - - libcurl=7.75.0 + - libcurl=7.76.0 - libdb=6.2.32 - libdeflate=1.7 - libedit=3.1.20191231 @@ -250,8 +249,8 @@ dependencies: - lzo=2.10 - markdown=3.3.4 - markupsafe=1.1.1 - - matplotlib=3.3.4 - - matplotlib-base=3.3.4 + - matplotlib=3.4.1 + - matplotlib-base=3.4.1 - mccabe=0.6.1 - mistune=0.8.4 - mock=4.0.3 @@ -275,7 +274,7 @@ dependencies: - nbconvert=6.0.7 - nbformat=5.1.2 - ncurses=6.2 - - nest-asyncio=1.4.3 + - nest-asyncio=1.5.1 - netifaces=0.10.9 - nettle=3.6 - networkx=2.5 @@ -308,7 +307,7 @@ dependencies: - pango=1.42.4 - papermill=2.3.3 - param=1.10.1 - - parso=0.8.1 + - parso=0.8.2 - partd=1.1.0 - patchelf=0.11 - pathspec=0.8.1 @@ -407,7 +406,7 @@ dependencies: - pywavelets=1.1.1 - pyyaml=5.4.1 - pyzmq=22.0.3 - - qdarkstyle=2.8.1 + - qdarkstyle=3.0.2 - qt=5.12.9 - qtawesome=1.0.2 - qtconsole=5.0.3 @@ -449,7 +448,7 @@ dependencies: - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.4 - - sqlalchemy=1.4.3 + - sqlalchemy=1.4.4 - sqlite=3.35.3 - statsmodels=0.12.2 - suitcase-mongo=0.2.0 From b284af9a49434fb762aad931a7f15aa690598b4e Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 13:18:59 -0700 Subject: [PATCH 03/11] MNT: temporarily freeze pydm version for today's tag --- envs/pcds/conda-packages.txt | 2 +- envs/pcds/keep-updated.txt | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index e7d81327..568691fc 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -52,7 +52,7 @@ psdm_qs_cli>=0.3.1 pswalker>=1.0.6 pyaudio pyca>=3.1.1 -pydm>=1.11.0 +pydm=1.10.7 pyepics>=3.4.3 pyfiglet pymongo diff --git a/envs/pcds/keep-updated.txt b/envs/pcds/keep-updated.txt index 367bfc71..2a1c6945 100644 --- a/envs/pcds/keep-updated.txt +++ b/envs/pcds/keep-updated.txt @@ -21,7 +21,6 @@ psdaq-control-minimal psdm_qs_cli pswalker pyca -pydm pyepics pytmc tc_release From 0ede5514193dd3f13fb3a42d7bdc19f35e20df44 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 16:59:58 -0700 Subject: [PATCH 04/11] MNT: update some dependency pins --- envs/pcds/conda-packages.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index 568691fc..90cf9413 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -40,9 +40,9 @@ panel papermill pcaspy pcdscalc>=0.2.0 -pcdsdaq>=2.3.3 -pcdsdevices>=4.2.0 -pcdsutils>=0.4.1 +pcdsdaq>=2.3.4 +pcdsdevices>=4.3.0 +pcdsutils>=0.4.2 pcdswidgets>=0.5.1 periodictable pmgr>=1.1.4 @@ -64,7 +64,7 @@ pytest-qt pytest-timeout python-graphviz python-ldap -pytmc>=2.8.1 +pytmc>=2.9.0 qdarkstyle scikit-image scikit-learn @@ -77,7 +77,7 @@ sphinx_rtd_theme tc_release>=0.2.1 timechart>=1.2.3 transfocate>=0.4.0 -typhos>=1.1.4 +typhos>=1.1.5 versioneer xarray xraylib From 36d01da4869c74e78fe9da6715f3dc26b1e51922 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 21:28:41 -0700 Subject: [PATCH 05/11] ENH: updated pcds to 4.1.0 --- envs/pcds/conda-packages.txt | 4 ++-- envs/pcds/env.yaml | 28 ++++++++++++++-------------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index 90cf9413..ada6620a 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -41,7 +41,7 @@ papermill pcaspy pcdscalc>=0.2.0 pcdsdaq>=2.3.4 -pcdsdevices>=4.3.0 +pcdsdevices>=4.3.1 pcdsutils>=0.4.2 pcdswidgets>=0.5.1 periodictable @@ -64,7 +64,7 @@ pytest-qt pytest-timeout python-graphviz python-ldap -pytmc>=2.9.0 +pytmc=2.8.1 qdarkstyle scikit-image scikit-learn diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index c200046d..89d84da5 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -76,18 +76,18 @@ dependencies: - cyrus-sasl=2.1.27 - cython=0.29.22 - cytoolz=0.11.0 - - dask=2021.3.1 - - dask-core=2021.3.1 + - dask=2021.4.0 + - dask-core=2021.4.0 - databroker=1.2.3 - dataclasses=0.8 - datashader=0.12.1 - datashape=0.5.4 - dbus=1.13.6 - - decorator=4.4.2 + - decorator=5.0.3 - defusedxml=0.7.1 - deprecated=1.2.10 - distlib=0.3.1 - - distributed=2021.3.1 + - distributed=2021.4.0 - docopt=0.6.2 - doct=1.1.0 - doctr=1.8.0 @@ -154,7 +154,7 @@ dependencies: - icu=68.1 - identify=2.1.4 - idna=2.10 - - imagecodecs=2021.1.28 + - imagecodecs=2021.3.31 - imageio=2.9.0 - imagesize=1.2.0 - importlib-metadata=3.10.0 @@ -272,7 +272,7 @@ dependencies: - nabs=1.1.1 - nbclient=0.5.3 - nbconvert=6.0.7 - - nbformat=5.1.2 + - nbformat=5.1.3 - ncurses=6.2 - nest-asyncio=1.5.1 - netifaces=0.10.9 @@ -314,9 +314,9 @@ dependencies: - patsy=0.5.1 - pcaspy=0.7.3 - pcdscalc=0.2.0 - - pcdsdaq=2.3.3 - - pcdsdevices=4.2.0 - - pcdsutils=0.4.1 + - pcdsdaq=2.3.4 + - pcdsdevices=4.3.1 + - pcdsutils=0.4.2 - pcdswidgets=0.5.1 - pcre=8.44 - periodictable=1.5.2 @@ -337,7 +337,7 @@ dependencies: - poyo=0.5.0 - pre-commit=2.11.1 - prettytable=2.1.0 - - prometheus_client=0.9.0 + - prometheus_client=0.10.0 - prompt-toolkit=3.0.18 - prompt_toolkit=3.0.18 - protobuf=3.15.6 @@ -366,7 +366,7 @@ dependencies: - pycrypto=2.6.1 - pyct=0.4.6 - pyct-core=0.4.6 - - pydm=1.11.0 + - pydm=1.10.7 - pyepics=3.4.3 - pyfiglet=0.8.post1 - pyflakes=2.3.1 @@ -448,7 +448,7 @@ dependencies: - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.4 - - sqlalchemy=1.4.4 + - sqlalchemy=1.4.5 - sqlite=3.35.3 - statsmodels=0.12.2 - suitcase-mongo=0.2.0 @@ -475,7 +475,7 @@ dependencies: - transitions=0.8.7 - trio=0.18.0 - typed-ast=1.4.2 - - typhos=1.1.4 + - typhos=1.1.5 - typing_extensions=3.7.4.3 - tzlocal=2.1 - uncertainties=3.1.5 @@ -516,4 +516,4 @@ dependencies: - zipp=3.4.1 - zlib=1.2.11 - zstd=1.4.9 -prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-4.1.0 +prefix: /cds/home/z/zlentz/miniconda3/envs/test-conda/envs/pcds-4.1.0 From 94ecb00c2d9241d7fb49e20f5900cbc1702a3474 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Fri, 2 Apr 2021 21:31:39 -0700 Subject: [PATCH 06/11] MNT: restore keep updated for next time --- envs/pcds/conda-packages.txt | 4 ++-- envs/pcds/keep-updated.txt | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index ada6620a..1b624afb 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -52,7 +52,7 @@ psdm_qs_cli>=0.3.1 pswalker>=1.0.6 pyaudio pyca>=3.1.1 -pydm=1.10.7 +pydm>=1.11.0 pyepics>=3.4.3 pyfiglet pymongo @@ -64,7 +64,7 @@ pytest-qt pytest-timeout python-graphviz python-ldap -pytmc=2.8.1 +pytmc>=2.9.0 qdarkstyle scikit-image scikit-learn diff --git a/envs/pcds/keep-updated.txt b/envs/pcds/keep-updated.txt index 2a1c6945..367bfc71 100644 --- a/envs/pcds/keep-updated.txt +++ b/envs/pcds/keep-updated.txt @@ -21,6 +21,7 @@ psdaq-control-minimal psdm_qs_cli pswalker pyca +pydm pyepics pytmc tc_release From 67516c4daef6ab6be2a5ba27164d81bf717a207a Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Tue, 6 Apr 2021 09:00:52 -0700 Subject: [PATCH 07/11] ENH: updated pcds to 4.1.0 --- envs/pcds/env.yaml | 515 +-------------------------------------------- 1 file changed, 1 insertion(+), 514 deletions(-) diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index 89d84da5..e41f413d 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -3,517 +3,4 @@ channels: - conda-forge - pcds-tag - lcls-ii -dependencies: - - _libgcc_mutex=0.1 - - _openmp_mutex=4.5 - - abseil-cpp=20200923.3 - - ads-async=0.1.0 - - alabaster=0.7.12 - - alsa-lib=1.2.3 - - amityping=1.1.6 - - anaconda-client=1.7.2 - - ansiwrap=0.8.4 - - appdirs=1.4.4 - - archapp=1.0.0 - - argon2-cffi=20.1.0 - - arrow=1.0.3 - - asciitree=0.3.3 - - asteval=0.9.23 - - async_generator=1.10 - - atk-1.0=2.36.0 - - attrs=20.3.0 - - babel=2.9.0 - - backcall=0.2.0 - - backports=1.0 - - backports.functools_lru_cache=1.6.3 - - beautifulsoup4=4.9.3 - - binaryornot=0.4.4 - - black=20.8b1 - - bleach=3.3.0 - - blinker=1.4 - - blosc=1.21.0 - - bluesky=1.6.7 - - bluesky-live=0.0.7 - - bokeh=2.3.0 - - boltons=20.2.1 - - boolean.py=3.7 - - boost-cpp=1.74.0 - - brotli=1.0.9 - - brotlipy=0.7.0 - - brunsli=0.1 - - bzip2=1.0.8 - - c-ares=1.17.1 - - ca-certificates=2020.12.5 - - cached-property=1.5.2 - - cached_property=1.5.2 - - cachetools=4.2.1 - - cairo=1.16.0 - - caproto=0.8.0 - - certifi=2020.12.5 - - cffi=1.14.5 - - cfgv=3.2.0 - - chardet=4.0.0 - - charls=2.2.0 - - click=7.1.2 - - cloudpickle=1.6.0 - - clyent=1.2.2 - - colorama=0.4.4 - - colorcet=2.0.6 - - coloredlogs=15.0 - - conda=4.10.0 - - conda-build=3.21.4 - - conda-forge-pinning=2021.04.02.15.43.00 - - conda-pack=0.6.0 - - conda-package-handling=1.7.2 - - conda-smithy=3.9.0 - - contextlib2=0.5.5 - - cookiecutter=1.7.2 - - coverage=5.5 - - cryptography=3.4.7 - - curio=1.4 - - curl=7.76.0 - - cycler=0.10.0 - - cyrus-sasl=2.1.27 - - cython=0.29.22 - - cytoolz=0.11.0 - - dask=2021.4.0 - - dask-core=2021.4.0 - - databroker=1.2.3 - - dataclasses=0.8 - - datashader=0.12.1 - - datashape=0.5.4 - - dbus=1.13.6 - - decorator=5.0.3 - - defusedxml=0.7.1 - - deprecated=1.2.10 - - distlib=0.3.1 - - distributed=2021.4.0 - - docopt=0.6.2 - - doct=1.1.0 - - doctr=1.8.0 - - docutils=0.16 - - dpkt=1.9.5 - - editdistance=0.5.3 - - elog=1.0.2 - - entrypoints=0.3 - - epics-base=7.0.5.0 - - epics-pypdb=0.1.5 - - epicscorelibs=7.0.3.99.4.0 - - et_xmlfile=1.0.1 - - event-model=1.17.1 - - expat=2.3.0 - - fasteners=0.14.1 - - ffmpeg=4.3.1 - - filelock=3.0.12 - - flake8=3.9.0 - - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=2.001 - - font-ttf-source-code-pro=2.030 - - font-ttf-ubuntu=0.83 - - fontconfig=2.13.1 - - fonts-conda-ecosystem=1 - - fonts-conda-forge=1 - - freetype=2.10.4 - - fribidi=1.0.10 - - fsspec=0.8.7 - - future=0.18.2 - - fuzzywuzzy=0.18.0 - - fzf=0.26.0 - - gdk-pixbuf=2.42.4 - - gettext=0.19.8.1 - - gh=1.6.2 - - giflib=5.2.1 - - git=2.30.2 - - gitdb=4.0.7 - - gitpython=3.1.14 - - glib=2.68.0 - - glib-tools=2.68.0 - - glob2=0.7 - - gmp=6.2.1 - - gnutls=3.6.13 - - graphite2=1.3.13 - - graphviz=2.47.0 - - greenlet=1.0.0 - - grpcio=1.33.2 - - grpcio-tools=1.33.2 - - gst-plugins-base=1.14.5 - - gstreamer=1.18.4 - - gtk2=2.24.33 - - gts=0.7.6 - - h5py=3.1.0 - - happi=1.9.0 - - harfbuzz=2.8.0 - - hdf5=1.10.6 - - heapdict=1.0.1 - - historydict=1.2.3 - - holoviews=1.14.2 - - humanfriendly=9.1 - - humanize=3.3.0 - - hutch-python=1.9.1 - - hxrsnd=0.2.4 - - icu=68.1 - - identify=2.1.4 - - idna=2.10 - - imagecodecs=2021.3.31 - - imageio=2.9.0 - - imagesize=1.2.0 - - importlib-metadata=3.10.0 - - importlib_metadata=3.10.0 - - importlib_resources=5.1.2 - - iniconfig=1.1.1 - - intake=0.6.2 - - ipykernel=5.5.3 - - ipython=7.22.0 - - ipython_genutils=0.2.0 - - ipywidgets=7.6.3 - - isodate=0.6.0 - - isort=5.8.0 - - jack=0.125.0 - - jasper=1.900.1 - - jdcal=1.4.1 - - jedi=0.18.0 - - jinja2=2.11.3 - - jinja2-time=0.2.0 - - joblib=1.0.1 - - jpeg=9d - - jsonschema=3.2.0 - - jupyter=1.0.0 - - jupyter_client=6.1.12 - - jupyter_console=6.4.0 - - jupyter_core=4.7.1 - - jupyterlab_pygments=0.1.2 - - jupyterlab_widgets=1.0.0 - - jxrlib=1.1 - - kiwisolver=1.3.1 - - krb5=1.17.2 - - krtc=0.1.4 - - lame=3.100 - - lcms2=2.12 - - ld_impl_linux-64=2.35.1 - - lerc=2.2.1 - - libaec=1.0.4 - - libarchive=3.5.1 - - libblas=3.9.0 - - libcblas=3.9.0 - - libclang=11.1.0 - - libcurl=7.76.0 - - libdb=6.2.32 - - libdeflate=1.7 - - libedit=3.1.20191231 - - libev=4.33 - - libevent=2.1.10 - - libffi=3.3 - - libgcc-ng=9.3.0 - - libgd=2.3.2 - - libgfortran-ng=9.3.0 - - libgfortran5=9.3.0 - - libglib=2.68.0 - - libgomp=9.3.0 - - libiconv=1.16 - - liblapack=3.9.0 - - liblapacke=3.9.0 - - liblief=0.10.1 - - libllvm10=10.0.1 - - libllvm11=11.1.0 - - libnghttp2=1.43.0 - - libntlm=1.4 - - libopenblas=0.3.12 - - libopencv=4.5.1 - - libpng=1.6.37 - - libpq=12.3 - - libprotobuf=3.15.6 - - librsvg=2.50.3 - - libsodium=1.0.18 - - libssh2=1.9.0 - - libstdcxx-ng=9.3.0 - - libtiff=4.2.0 - - libtool=2.4.6 - - libunwind=1.4.0 - - libuuid=2.32.1 - - libwebp=1.2.0 - - libwebp-base=1.2.0 - - libxcb=1.13 - - libxkbcommon=1.0.3 - - libxml2=2.9.10 - - libxslt=1.1.33 - - libzopfli=1.0.3 - - license-expression=1.2 - - lightpath=0.6.8 - - line_profiler=3.1.0 - - llvmlite=0.36.0 - - lmfit=1.0.2 - - locket=0.2.0 - - lucid=0.7.2 - - lxml=4.6.3 - - lz4-c=1.9.3 - - lzo=2.10 - - markdown=3.3.4 - - markupsafe=1.1.1 - - matplotlib=3.4.1 - - matplotlib-base=3.4.1 - - mccabe=0.6.1 - - mistune=0.8.4 - - mock=4.0.3 - - mongodb=4.2.13 - - mongoquery=1.3.5 - - monotonic=1.5 - - more-itertools=8.7.0 - - mpi=1.0 - - mpi4py=3.0.3 - - mpich=3.4.1 - - msgpack-numpy=0.4.7.1 - - msgpack-python=1.0.2 - - msrest=0.6.21 - - multipledispatch=0.6.0 - - mypy_extensions=0.4.3 - - mysql-common=8.0.22 - - mysql-libs=8.0.22 - - mysqlclient=2.0.3 - - nabs=1.1.1 - - nbclient=0.5.3 - - nbconvert=6.0.7 - - nbformat=5.1.3 - - ncurses=6.2 - - nest-asyncio=1.5.1 - - netifaces=0.10.9 - - nettle=3.6 - - networkx=2.5 - - nodeenv=1.5.0 - - nose=1.3.7 - - notebook=6.3.0 - - nspr=4.30 - - nss=3.63 - - numba=0.53.1 - - numcodecs=0.7.3 - - numexpr=2.7.3 - - numpy=1.20.2 - - numpydoc=1.1.0 - - oauthlib=3.0.1 - - olefile=0.46 - - opencv=4.5.1 - - openh264=2.1.1 - - openjpeg=2.4.0 - - openldap=2.4.52 - - openpyxl=3.0.7 - - openssl=1.1.1k - - ophyd=1.6.1 - - outcome=1.1.0 - - p4p=3.5.2 - - packaging=20.9 - - pandas=1.2.3 - - pandoc=2.12 - - pandocfilters=1.4.2 - - panel=0.11.1 - - pango=1.42.4 - - papermill=2.3.3 - - param=1.10.1 - - parso=0.8.2 - - partd=1.1.0 - - patchelf=0.11 - - pathspec=0.8.1 - - patsy=0.5.1 - - pcaspy=0.7.3 - - pcdscalc=0.2.0 - - pcdsdaq=2.3.4 - - pcdsdevices=4.3.1 - - pcdsutils=0.4.2 - - pcdswidgets=0.5.1 - - pcre=8.44 - - periodictable=1.5.2 - - perl=5.32.0 - - pexpect=4.8.0 - - pickleshare=0.7.5 - - pillow=8.1.2 - - pims=0.5 - - pint=0.17 - - pip=21.0.1 - - pixman=0.40.0 - - pkginfo=1.7.0 - - pluggy=0.13.1 - - ply=3.11 - - pmgr=1.1.4 - - pooch=1.3.0 - - portaudio=19.6.0 - - poyo=0.5.0 - - pre-commit=2.11.1 - - prettytable=2.1.0 - - prometheus_client=0.10.0 - - prompt-toolkit=3.0.18 - - prompt_toolkit=3.0.18 - - protobuf=3.15.6 - - psalg=3.3.14 - - psana=3.3.14 - - psdaq-control-minimal=3.3.14 - - psdm_qs_cli=0.3.1 - - psmon=1.0.2 - - psutil=5.8.0 - - pswalker=1.0.6 - - pthread-stubs=0.4 - - ptyprocess=0.7.0 - - py=1.10.0 - - py-cpuinfo=7.0.0 - - py-lief=0.10.1 - - py-opencv=4.5.1 - - py-spy=0.3.4 - - pyabel=0.8.3 - - pyasn1=0.4.8 - - pyasn1-modules=0.2.7 - - pyaudio=0.2.11 - - pyca=3.1.1 - - pycodestyle=2.7.0 - - pycosat=0.6.3 - - pycparser=2.20 - - pycrypto=2.6.1 - - pyct=0.4.6 - - pyct-core=0.4.6 - - pydm=1.10.7 - - pyepics=3.4.3 - - pyfiglet=0.8.post1 - - pyflakes=2.3.1 - - pygithub=1.53 - - pygments=2.8.1 - - pyjwt=2.0.1 - - pykerberos=1.2.1 - - pymongo=3.11.0 - - pyopenssl=20.0.1 - - pypandoc=1.5 - - pyparsing=2.4.7 - - pyqt=5.12.3 - - pyqt-impl=5.12.3 - - pyqt5-sip=4.19.18 - - pyqtads=3.7.0 - - pyqtchart=5.12 - - pyqtgraph=0.12.0 - - pyqtwebengine=5.12.1 - - pyrsistent=0.17.3 - - pysocks=1.7.1 - - pytables=3.6.1 - - pytest=6.2.2 - - pytest-benchmark=3.2.3 - - pytest-qt=3.3.0 - - pytest-timeout=1.4.2 - - python=3.8.8 - - python-dateutil=2.8.1 - - python-graphviz=0.16 - - python-ldap=3.3.1 - - python-levenshtein=0.12.2 - - python-libarchive-c=2.9 - - python-slugify=4.0.1 - - python_abi=3.8 - - pytmc=2.8.1 - - pytz=2021.1 - - pyviz_comms=2.0.1 - - pywavelets=1.1.1 - - pyyaml=5.4.1 - - pyzmq=22.0.3 - - qdarkstyle=3.0.2 - - qt=5.12.9 - - qtawesome=1.0.2 - - qtconsole=5.0.3 - - qtpy=1.9.0 - - qtpyinheritance=0.0.1 - - readline=8.0 - - regex=2021.3.17 - - requests=2.25.1 - - requests-oauthlib=1.3.0 - - ripgrep=12.1.1 - - roentdek=0.0.3 - - ruamel.yaml=0.16.12 - - ruamel.yaml.clib=0.2.2 - - ruamel_yaml=0.15.80 - - schema=0.7.4 - - scikit-image=0.18.1 - - scikit-learn=0.24.1 - - scipy=1.6.2 - - scrypt=0.8.17 - - seaborn=0.11.1 - - seaborn-base=0.11.1 - - send2trash=1.5.0 - - setuptools=49.6.0 - - shellcheck=0.7.1 - - simplejson=3.17.2 - - six=1.15.0 - - slicerator=1.0.0 - - smmap=3.0.5 - - snappy=1.1.8 - - sniffio=1.2.0 - - snowballstemmer=2.1.0 - - sortedcontainers=2.3.0 - - soupsieve=2.0.1 - - sphinx=3.5.3 - - sphinx_rtd_theme=0.5.1 - - sphinxcontrib-applehelp=1.0.2 - - sphinxcontrib-devhelp=1.0.2 - - sphinxcontrib-htmlhelp=1.0.3 - - sphinxcontrib-jsmath=1.0.1 - - sphinxcontrib-qthelp=1.0.3 - - sphinxcontrib-serializinghtml=1.1.4 - - sqlalchemy=1.4.5 - - sqlite=3.35.3 - - statsmodels=0.12.2 - - suitcase-mongo=0.2.0 - - suitcase-msgpack=0.2.4 - - suitcase-utils=0.5.3 - - super_state_machine=2.0.2 - - tblib=1.7.0 - - tc_release=0.2.1 - - tenacity=7.0.0 - - terminado=0.9.4 - - testpath=0.4.4 - - text-unidecode=1.3 - - textwrap3=0.9.2 - - threadpoolctl=2.1.0 - - tifffile=2021.3.17 - - timechart=1.2.3 - - tk=8.6.10 - - toml=0.10.2 - - toolz=0.11.1 - - tornado=6.1 - - tqdm=4.59.0 - - traitlets=5.0.5 - - transfocate=0.4.0 - - transitions=0.8.7 - - trio=0.18.0 - - typed-ast=1.4.2 - - typhos=1.1.5 - - typing_extensions=3.7.4.3 - - tzlocal=2.1 - - uncertainties=3.1.5 - - unidecode=1.2.0 - - urllib3=1.26.4 - - versioneer=0.19 - - virtualenv=20.4.3 - - vsts-python-api=0.1.22 - - wcwidth=0.2.5 - - webencodings=0.5.1 - - wheel=0.36.2 - - whichcraft=0.6.1 - - widgetsnbextension=3.5.1 - - wrapt=1.12.1 - - x264=1!161.3030 - - xarray=0.17.0 - - xorg-kbproto=1.0.7 - - xorg-libice=1.0.10 - - xorg-libsm=1.2.3 - - xorg-libx11=1.7.0 - - xorg-libxau=1.0.9 - - xorg-libxdmcp=1.1.3 - - xorg-libxext=1.3.4 - - xorg-libxrender=0.9.10 - - xorg-renderproto=0.11.1 - - xorg-xextproto=7.3.0 - - xorg-xproto=7.0.31 - - xraydb=4.4.5 - - xraylib=4.0.0 - - xtcdata=3.3.14 - - xz=5.2.5 - - yaml=0.2.5 - - yaml-cpp=0.6.3 - - zarr=2.7.0 - - zeromq=4.3.4 - - zfp=0.5.5 - - zict=2.0.0 - - zipp=3.4.1 - - zlib=1.2.11 - - zstd=1.4.9 -prefix: /cds/home/z/zlentz/miniconda3/envs/test-conda/envs/pcds-4.1.0 +prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-4.1.0 From 6d26b82e7059766dbfd7f4c9d066edc3a622db56 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Tue, 6 Apr 2021 09:35:43 -0700 Subject: [PATCH 08/11] ENH: updated pcds to 4.1.0 --- envs/pcds/conda-packages.txt | 6 +- envs/pcds/env.yaml | 513 +++++++++++++++++++++++++++++++++++ 2 files changed, 516 insertions(+), 3 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index 1b624afb..f22cb4b9 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -41,7 +41,7 @@ papermill pcaspy pcdscalc>=0.2.0 pcdsdaq>=2.3.4 -pcdsdevices>=4.3.1 +pcdsdevices>=4.3.2 pcdsutils>=0.4.2 pcdswidgets>=0.5.1 periodictable @@ -75,9 +75,9 @@ simplejson sphinx sphinx_rtd_theme tc_release>=0.2.1 -timechart>=1.2.3 +timechart>=1.2.4 transfocate>=0.4.0 -typhos>=1.1.5 +typhos>=1.1.6 versioneer xarray xraylib diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index e41f413d..566e9ef1 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -3,4 +3,517 @@ channels: - conda-forge - pcds-tag - lcls-ii +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - abseil-cpp=20200923.3 + - ads-async=0.1.0 + - alabaster=0.7.12 + - alsa-lib=1.2.3 + - amityping=1.1.6 + - anaconda-client=1.7.2 + - ansiwrap=0.8.4 + - appdirs=1.4.4 + - archapp=1.0.0 + - argon2-cffi=20.1.0 + - arrow=1.0.3 + - asciitree=0.3.3 + - asteval=0.9.23 + - async_generator=1.10 + - atk-1.0=2.36.0 + - attrs=20.3.0 + - babel=2.9.0 + - backcall=0.2.0 + - backports=1.0 + - backports.functools_lru_cache=1.6.3 + - beautifulsoup4=4.9.3 + - binaryornot=0.4.4 + - black=20.8b1 + - bleach=3.3.0 + - blinker=1.4 + - blosc=1.21.0 + - bluesky=1.6.7 + - bluesky-live=0.0.7 + - bokeh=2.3.0 + - boltons=20.2.1 + - boolean.py=3.7 + - boost-cpp=1.74.0 + - brotli=1.0.9 + - brotlipy=0.7.0 + - brunsli=0.1 + - bzip2=1.0.8 + - c-ares=1.17.1 + - ca-certificates=2020.12.5 + - cached-property=1.5.2 + - cached_property=1.5.2 + - cachetools=4.2.1 + - cairo=1.16.0 + - caproto=0.8.0 + - certifi=2020.12.5 + - cffi=1.14.5 + - cfgv=3.2.0 + - chardet=4.0.0 + - charls=2.2.0 + - click=7.1.2 + - cloudpickle=1.6.0 + - clyent=1.2.2 + - colorama=0.4.4 + - colorcet=2.0.6 + - coloredlogs=15.0 + - conda=4.10.0 + - conda-build=3.21.4 + - conda-forge-pinning=2021.04.06.13.31.20 + - conda-pack=0.6.0 + - conda-package-handling=1.7.2 + - conda-smithy=3.9.0 + - contextlib2=0.5.5 + - cookiecutter=1.7.2 + - coverage=5.5 + - cryptography=3.4.7 + - curio=1.4 + - curl=7.76.0 + - cycler=0.10.0 + - cyrus-sasl=2.1.27 + - cython=0.29.22 + - cytoolz=0.11.0 + - dask=2021.4.0 + - dask-core=2021.4.0 + - databroker=1.2.3 + - dataclasses=0.8 + - datashader=0.12.1 + - datashape=0.5.4 + - dbus=1.13.6 + - decorator=5.0.5 + - defusedxml=0.7.1 + - deprecated=1.2.10 + - distlib=0.3.1 + - distributed=2021.4.0 + - docopt=0.6.2 + - doct=1.1.0 + - doctr=1.8.0 + - docutils=0.17 + - dpkt=1.9.5 + - editdistance=0.5.3 + - elog=1.0.2 + - entrypoints=0.3 + - epics-base=7.0.5.0 + - epics-pypdb=0.1.5 + - epicscorelibs=7.0.3.99.4.0 + - et_xmlfile=1.0.1 + - event-model=1.17.1 + - expat=2.3.0 + - fasteners=0.14.1 + - ffmpeg=4.3.1 + - filelock=3.0.12 + - flake8=3.9.0 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=2.001 + - font-ttf-source-code-pro=2.030 + - font-ttf-ubuntu=0.83 + - fontconfig=2.13.1 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - freetype=2.10.4 + - fribidi=1.0.10 + - fsspec=0.9.0 + - future=0.18.2 + - fuzzywuzzy=0.18.0 + - fzf=0.26.0 + - gdk-pixbuf=2.42.4 + - gettext=0.19.8.1 + - gh=1.6.2 + - giflib=5.2.1 + - git=2.30.2 + - gitdb=4.0.7 + - gitpython=3.1.14 + - glib=2.68.0 + - glib-tools=2.68.0 + - glob2=0.7 + - gmp=6.2.1 + - gnutls=3.6.13 + - graphite2=1.3.13 + - graphviz=2.47.0 + - greenlet=1.0.0 + - grpcio=1.33.2 + - grpcio-tools=1.33.2 + - gst-plugins-base=1.14.5 + - gstreamer=1.18.4 + - gtk2=2.24.33 + - gts=0.7.6 + - h5py=3.1.0 + - happi=1.9.0 + - harfbuzz=2.8.0 + - hdf5=1.10.6 + - heapdict=1.0.1 + - historydict=1.2.3 + - holoviews=1.14.2 + - humanfriendly=9.1 + - humanize=3.3.0 + - hutch-python=1.9.1 + - hxrsnd=0.2.4 + - icu=68.1 + - identify=2.1.4 + - idna=2.10 + - imagecodecs=2021.3.31 + - imageio=2.9.0 + - imagesize=1.2.0 + - importlib-metadata=3.10.0 + - importlib_metadata=3.10.0 + - importlib_resources=5.1.2 + - iniconfig=1.1.1 + - intake=0.6.2 + - ipykernel=5.5.3 + - ipython=7.22.0 + - ipython_genutils=0.2.0 + - ipywidgets=7.6.3 + - isodate=0.6.0 + - isort=5.8.0 + - jack=0.125.0 + - jasper=1.900.1 + - jdcal=1.4.1 + - jedi=0.18.0 + - jinja2=2.11.3 + - jinja2-time=0.2.0 + - joblib=1.0.1 + - jpeg=9d + - jsonschema=3.2.0 + - jupyter=1.0.0 + - jupyter_client=6.1.12 + - jupyter_console=6.4.0 + - jupyter_core=4.7.1 + - jupyterlab_pygments=0.1.2 + - jupyterlab_widgets=1.0.0 + - jxrlib=1.1 + - kiwisolver=1.3.1 + - krb5=1.17.2 + - krtc=0.1.4 + - lame=3.100 + - lcms2=2.12 + - ld_impl_linux-64=2.35.1 + - lerc=2.2.1 + - libaec=1.0.4 + - libarchive=3.5.1 + - libblas=3.9.0 + - libcblas=3.9.0 + - libclang=11.1.0 + - libcurl=7.76.0 + - libdb=6.2.32 + - libdeflate=1.7 + - libedit=3.1.20191231 + - libev=4.33 + - libevent=2.1.10 + - libffi=3.3 + - libgcc-ng=9.3.0 + - libgd=2.3.2 + - libgfortran-ng=9.3.0 + - libgfortran5=9.3.0 + - libglib=2.68.0 + - libgomp=9.3.0 + - libiconv=1.16 + - liblapack=3.9.0 + - liblapacke=3.9.0 + - liblief=0.10.1 + - libllvm10=10.0.1 + - libllvm11=11.1.0 + - libnghttp2=1.43.0 + - libntlm=1.4 + - libopenblas=0.3.12 + - libopencv=4.5.1 + - libpng=1.6.37 + - libpq=12.3 + - libprotobuf=3.15.7 + - librsvg=2.50.3 + - libsodium=1.0.18 + - libssh2=1.9.0 + - libstdcxx-ng=9.3.0 + - libtiff=4.2.0 + - libtool=2.4.6 + - libunwind=1.4.0 + - libuuid=2.32.1 + - libwebp=1.2.0 + - libwebp-base=1.2.0 + - libxcb=1.13 + - libxkbcommon=1.0.3 + - libxml2=2.9.10 + - libxslt=1.1.33 + - libzopfli=1.0.3 + - license-expression=1.2 + - lightpath=0.6.8 + - line_profiler=3.1.0 + - llvmlite=0.36.0 + - lmfit=1.0.2 + - locket=0.2.0 + - lucid=0.7.2 + - lxml=4.6.3 + - lz4-c=1.9.3 + - lzo=2.10 + - markdown=3.3.4 + - markupsafe=1.1.1 + - matplotlib=3.4.1 + - matplotlib-base=3.4.1 + - mccabe=0.6.1 + - mistune=0.8.4 + - mock=4.0.3 + - mongodb=4.2.13 + - mongoquery=1.3.5 + - monotonic=1.5 + - more-itertools=8.7.0 + - mpi=1.0 + - mpi4py=3.0.3 + - mpich=3.4.1 + - msgpack-numpy=0.4.7.1 + - msgpack-python=1.0.2 + - msrest=0.6.21 + - multipledispatch=0.6.0 + - mypy_extensions=0.4.3 + - mysql-common=8.0.22 + - mysql-libs=8.0.22 + - mysqlclient=2.0.3 + - nabs=1.1.1 + - nbclient=0.5.3 + - nbconvert=6.0.7 + - nbformat=5.1.3 + - ncurses=6.2 + - nest-asyncio=1.5.1 + - netifaces=0.10.9 + - nettle=3.6 + - networkx=2.5 + - nodeenv=1.5.0 + - nose=1.3.7 + - notebook=6.3.0 + - nspr=4.30 + - nss=3.63 + - numba=0.53.1 + - numcodecs=0.7.3 + - numexpr=2.7.3 + - numpy=1.20.2 + - numpydoc=1.1.0 + - oauthlib=3.0.1 + - olefile=0.46 + - opencv=4.5.1 + - openh264=2.1.1 + - openjpeg=2.4.0 + - openldap=2.4.52 + - openpyxl=3.0.7 + - openssl=1.1.1k + - ophyd=1.6.1 + - outcome=1.1.0 + - p4p=3.5.2 + - packaging=20.9 + - pandas=1.2.3 + - pandoc=2.12 + - pandocfilters=1.4.2 + - panel=0.11.1 + - pango=1.42.4 + - papermill=2.3.3 + - param=1.10.1 + - parso=0.8.2 + - partd=1.1.0 + - patchelf=0.11 + - pathspec=0.8.1 + - patsy=0.5.1 + - pcaspy=0.7.3 + - pcdscalc=0.2.0 + - pcdsdaq=2.3.4 + - pcdsdevices=4.3.2 + - pcdsutils=0.4.2 + - pcdswidgets=0.5.1 + - pcre=8.44 + - periodictable=1.5.2 + - perl=5.32.0 + - pexpect=4.8.0 + - pickleshare=0.7.5 + - pillow=8.1.2 + - pims=0.5 + - pint=0.17 + - pip=21.0.1 + - pixman=0.40.0 + - pkginfo=1.7.0 + - pluggy=0.13.1 + - ply=3.11 + - pmgr=1.1.4 + - pooch=1.3.0 + - portaudio=19.6.0 + - poyo=0.5.0 + - pre-commit=2.11.1 + - prettytable=2.1.0 + - prometheus_client=0.10.0 + - prompt-toolkit=3.0.18 + - prompt_toolkit=3.0.18 + - protobuf=3.15.7 + - psalg=3.3.14 + - psana=3.3.14 + - psdaq-control-minimal=3.3.14 + - psdm_qs_cli=0.3.1 + - psmon=1.0.2 + - psutil=5.8.0 + - pswalker=1.0.6 + - pthread-stubs=0.4 + - ptyprocess=0.7.0 + - py=1.10.0 + - py-cpuinfo=7.0.0 + - py-lief=0.10.1 + - py-opencv=4.5.1 + - py-spy=0.3.4 + - pyabel=0.8.3 + - pyasn1=0.4.8 + - pyasn1-modules=0.2.7 + - pyaudio=0.2.11 + - pyca=3.1.1 + - pycodestyle=2.7.0 + - pycosat=0.6.3 + - pycparser=2.20 + - pycrypto=2.6.1 + - pyct=0.4.6 + - pyct-core=0.4.6 + - pydm=1.11.0 + - pyepics=3.4.3 + - pyfiglet=0.8.post1 + - pyflakes=2.3.1 + - pygithub=1.53 + - pygments=2.8.1 + - pyjwt=2.0.1 + - pykerberos=1.2.1 + - pymongo=3.11.0 + - pyopenssl=20.0.1 + - pypandoc=1.5 + - pyparsing=2.4.7 + - pyqt=5.12.3 + - pyqt-impl=5.12.3 + - pyqt5-sip=4.19.18 + - pyqtads=3.7.0 + - pyqtchart=5.12 + - pyqtgraph=0.12.0 + - pyqtwebengine=5.12.1 + - pyrsistent=0.17.3 + - pysocks=1.7.1 + - pytables=3.6.1 + - pytest=6.2.3 + - pytest-benchmark=3.2.3 + - pytest-qt=3.3.0 + - pytest-timeout=1.4.2 + - python=3.8.8 + - python-dateutil=2.8.1 + - python-graphviz=0.16 + - python-ldap=3.3.1 + - python-levenshtein=0.12.2 + - python-libarchive-c=2.9 + - python-slugify=4.0.1 + - python_abi=3.8 + - pytmc=2.9.0 + - pytz=2021.1 + - pyviz_comms=2.0.1 + - pywavelets=1.1.1 + - pyyaml=5.4.1 + - pyzmq=22.0.3 + - qdarkstyle=3.0.2 + - qt=5.12.9 + - qtawesome=1.0.2 + - qtconsole=5.0.3 + - qtpy=1.9.0 + - qtpyinheritance=0.0.1 + - readline=8.0 + - regex=2021.4.4 + - requests=2.25.1 + - requests-oauthlib=1.3.0 + - ripgrep=12.1.1 + - roentdek=0.0.3 + - ruamel.yaml=0.16.12 + - ruamel.yaml.clib=0.2.2 + - ruamel_yaml=0.15.80 + - schema=0.7.4 + - scikit-image=0.18.1 + - scikit-learn=0.24.1 + - scipy=1.6.2 + - scrypt=0.8.17 + - seaborn=0.11.1 + - seaborn-base=0.11.1 + - send2trash=1.5.0 + - setuptools=49.6.0 + - shellcheck=0.7.1 + - simplejson=3.17.2 + - six=1.15.0 + - slicerator=1.0.0 + - smmap=3.0.5 + - snappy=1.1.8 + - sniffio=1.2.0 + - snowballstemmer=2.1.0 + - sortedcontainers=2.3.0 + - soupsieve=2.0.1 + - sphinx=3.5.3 + - sphinx_rtd_theme=0.5.2 + - sphinxcontrib-applehelp=1.0.2 + - sphinxcontrib-devhelp=1.0.2 + - sphinxcontrib-htmlhelp=1.0.3 + - sphinxcontrib-jsmath=1.0.1 + - sphinxcontrib-qthelp=1.0.3 + - sphinxcontrib-serializinghtml=1.1.4 + - sqlalchemy=1.4.5 + - sqlite=3.35.4 + - statsmodels=0.12.2 + - suitcase-mongo=0.2.0 + - suitcase-msgpack=0.2.4 + - suitcase-utils=0.5.3 + - super_state_machine=2.0.2 + - tblib=1.7.0 + - tc_release=0.2.1 + - tenacity=7.0.0 + - terminado=0.9.4 + - testpath=0.4.4 + - text-unidecode=1.3 + - textwrap3=0.9.2 + - threadpoolctl=2.1.0 + - tifffile=2021.3.31 + - timechart=1.2.4 + - tk=8.6.10 + - toml=0.10.2 + - toolz=0.11.1 + - tornado=6.1 + - tqdm=4.60.0 + - traitlets=5.0.5 + - transfocate=0.4.0 + - transitions=0.8.7 + - trio=0.18.0 + - typed-ast=1.4.2 + - typhos=1.1.6 + - typing_extensions=3.7.4.3 + - tzlocal=2.1 + - uncertainties=3.1.5 + - unidecode=1.2.0 + - urllib3=1.26.4 + - versioneer=0.19 + - virtualenv=20.4.3 + - vsts-python-api=0.1.22 + - wcwidth=0.2.5 + - webencodings=0.5.1 + - wheel=0.36.2 + - whichcraft=0.6.1 + - widgetsnbextension=3.5.1 + - wrapt=1.12.1 + - x264=1!161.3030 + - xarray=0.17.0 + - xorg-kbproto=1.0.7 + - xorg-libice=1.0.10 + - xorg-libsm=1.2.3 + - xorg-libx11=1.7.0 + - xorg-libxau=1.0.9 + - xorg-libxdmcp=1.1.3 + - xorg-libxext=1.3.4 + - xorg-libxrender=0.9.10 + - xorg-renderproto=0.11.1 + - xorg-xextproto=7.3.0 + - xorg-xproto=7.0.31 + - xraydb=4.4.5 + - xraylib=4.0.0 + - xtcdata=3.3.14 + - xz=5.2.5 + - yaml=0.2.5 + - yaml-cpp=0.6.3 + - zarr=2.7.0 + - zeromq=4.3.4 + - zfp=0.5.5 + - zict=2.0.0 + - zipp=3.4.1 + - zlib=1.2.11 + - zstd=1.4.9 prefix: /cds/home/z/zlentz/miniconda3/envs/pcds-4.1.0 From 59bccd1c21a84a6bb49c08254ab955b4647d5e33 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Tue, 6 Apr 2021 10:13:34 -0700 Subject: [PATCH 09/11] MNT: pin docutils to 0.16 while compatibility issues are resolved --- envs/pcds/conda-packages.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index f22cb4b9..0ad82858 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -12,6 +12,7 @@ coverage databroker>=1.2.3 datashader doctr +docutils=0.16 elog>=1.0.2 epicscorelibs=7.0.3.99.4.0 flake8 From 8c364a095f6ec2bc64c1ed0882cec093b5619289 Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Tue, 6 Apr 2021 10:31:25 -0700 Subject: [PATCH 10/11] ENH: updated pcds to 4.1.0 --- envs/pcds/env.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index 566e9ef1..779c51cc 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -91,7 +91,7 @@ dependencies: - docopt=0.6.2 - doct=1.1.0 - doctr=1.8.0 - - docutils=0.17 + - docutils=0.16 - dpkt=1.9.5 - editdistance=0.5.3 - elog=1.0.2 From 78d942de3511bbc23132ce9ddb4cb63cf7536bcb Mon Sep 17 00:00:00 2001 From: Zachary Lentz Date: Wed, 7 Apr 2021 09:23:38 -0700 Subject: [PATCH 11/11] ENH: updated pcds to 4.1.0 --- envs/pcds/conda-packages.txt | 2 +- envs/pcds/env.yaml | 15 ++++++++------- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/envs/pcds/conda-packages.txt b/envs/pcds/conda-packages.txt index 0ad82858..a4a933d4 100644 --- a/envs/pcds/conda-packages.txt +++ b/envs/pcds/conda-packages.txt @@ -77,7 +77,7 @@ sphinx sphinx_rtd_theme tc_release>=0.2.1 timechart>=1.2.4 -transfocate>=0.4.0 +transfocate>=0.5.0 typhos>=1.1.6 versioneer xarray diff --git a/envs/pcds/env.yaml b/envs/pcds/env.yaml index 779c51cc..c659d547 100644 --- a/envs/pcds/env.yaml +++ b/envs/pcds/env.yaml @@ -62,7 +62,7 @@ dependencies: - coloredlogs=15.0 - conda=4.10.0 - conda-build=3.21.4 - - conda-forge-pinning=2021.04.06.13.31.20 + - conda-forge-pinning=2021.04.06.19.11.00 - conda-pack=0.6.0 - conda-package-handling=1.7.2 - conda-smithy=3.9.0 @@ -118,7 +118,7 @@ dependencies: - fsspec=0.9.0 - future=0.18.2 - fuzzywuzzy=0.18.0 - - fzf=0.26.0 + - fzf=0.27.0 - gdk-pixbuf=2.42.4 - gettext=0.19.8.1 - gh=1.6.2 @@ -335,7 +335,7 @@ dependencies: - pooch=1.3.0 - portaudio=19.6.0 - poyo=0.5.0 - - pre-commit=2.11.1 + - pre-commit=2.12.0 - prettytable=2.1.0 - prometheus_client=0.10.0 - prompt-toolkit=3.0.18 @@ -383,7 +383,7 @@ dependencies: - pyqt5-sip=4.19.18 - pyqtads=3.7.0 - pyqtchart=5.12 - - pyqtgraph=0.12.0 + - pyqtgraph=0.12.1 - pyqtwebengine=5.12.1 - pyrsistent=0.17.3 - pysocks=1.7.1 @@ -414,6 +414,7 @@ dependencies: - qtpyinheritance=0.0.1 - readline=8.0 - regex=2021.4.4 + - reportlab=3.5.66 - requests=2.25.1 - requests-oauthlib=1.3.0 - ripgrep=12.1.1 @@ -448,7 +449,7 @@ dependencies: - sphinxcontrib-jsmath=1.0.1 - sphinxcontrib-qthelp=1.0.3 - sphinxcontrib-serializinghtml=1.1.4 - - sqlalchemy=1.4.5 + - sqlalchemy=1.4.6 - sqlite=3.35.4 - statsmodels=0.12.2 - suitcase-mongo=0.2.0 @@ -471,8 +472,8 @@ dependencies: - tornado=6.1 - tqdm=4.60.0 - traitlets=5.0.5 - - transfocate=0.4.0 - - transitions=0.8.7 + - transfocate=0.5.0 + - transitions=0.8.8 - trio=0.18.0 - typed-ast=1.4.2 - typhos=1.1.6