update packaging requirements #313

prjemian · 2020-05-07T05:12:12Z

with new releases of upstream components

prjemian · 2020-05-07T13:26:13Z

Only include the packages that directly imported by apstools that are not in the standard python libraries. Each package manages its own set of requirements.

prjemian · 2020-05-07T14:46:53Z

still problems when trying conda install

conda config --set unsatisfiable_hints True
conda install "apstools=1.2.3rc2" -c aps-anl-tag -v

Collecting package metadata (current_repodata.json): ...working... Unable to retrieve repodata (response: 404) for https://conda.anaconda.org/aps-anl-tag/linux-64/current_repodata.json

Unable to retrieve repodata (response: 404) for https://conda.anaconda.org/prjemian/linux-64/current_repodata.json

Unable to retrieve repodata (response: 404) for https://conda.anaconda.org/nexpy/linux-64/current_repodata.json

Unable to retrieve repodata (response: 404) for https://conda.anaconda.org/aps-anl-dev/linux-64/current_repodata.json

done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... 
Building graph of deps:   0%|          | 0/3 [00:00<?, ?it/s]
Examining apstools=1.2.3rc2:   0%|          | 0/3 [00:00<?, ?it/s]
Examining @/linux-64::__glibc==2.23=0:  33%|███▎      | 1/3 [00:00<00:00,  3.86it/s]
Examining @/linux-64::__glibc==2.23=0:  67%|██████▋   | 2/3 [00:00<00:00,  7.71it/s]
Examining python=3.7:  67%|██████▋   | 2/3 [00:00<00:00,  7.71it/s]                 
                                                                   

Determining conflicts:   0%|          | 0/3 [00:00<?, ?it/s]
Examining conflict for apstools python:   0%|          | 0/3 [00:00<?, ?it/s]
                                                                             
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

Traceback (most recent call last):
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/install.py", line 265, in install
    should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
    ssc = self._run_sat(ssc)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
    should_retry_solve=ssc.should_retry_solve
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/resolve.py", line 1316, in solve
    raise UnsatisfiableError({})
conda.exceptions.UnsatisfiableError: 
Did not find conflicting dependencies. If you would like to know which
packages conflict ensure that you have enabled unsatisfiable hints.

conda config --set unsatisfiable_hints True
            

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/install.py", line 308, in install
    raise e
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/cli/install.py", line 299, in install
    should_retry_solve=(repodata_fn != repodata_fns[-1]),
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 275, in solve_final_state
    ssc = self._add_specs(ssc)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/core/solve.py", line 694, in _add_specs
    ssc.r.find_conflicts(spec_set)
  File "/home/prjemian/Apps/anaconda/lib/python3.7/site-packages/conda/resolve.py", line 351, in find_conflicts
    raise UnsatisfiableError(bad_deps, strict=strict_channel_priority)
conda.exceptions.UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

summary: still not installable

prjemian · 2020-05-07T14:48:22Z

Even, conda install apstools -c aps-anl-tag installs 1.1.16 but latest is 1.2.2 (or 1.2.3rc2). Clearly something has been wrong for a while.

prjemian · 2020-05-07T15:24:36Z

Here's a more certain test if the specified release can be installed:

(bluesky_2020_5) prjemian@poof ~ $ conda create -n apstools "apstools=1.2.3rc2" -c defaults -c conda-forge -c aps-anl-tag -nsls2forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                                                                                     failed

UnsatisfiableError:

prjemian · 2020-05-07T15:29:00Z

Release 1.1.16 is installed now if version not specified. What changed since? See commit hash 39a7ddc

prjemian · 2020-05-07T15:48:53Z

Fix the typo in previous command, change -nsls2forge to -c nsls2forge, here's the solved package list to install:

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  apstools           aps-anl-dev/noarch::apstools-1.2.3rc2-py_0
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.3.0-py38_0
  asteval            conda-forge/noarch::asteval-0.9.16-pyh5ca1d4c_0
  attrs              pkgs/main/noarch::attrs-19.3.0-py_0
  backcall           pkgs/main/linux-64::backcall-0.1.0-py38_0
  blas               pkgs/main/linux-64::blas-1.0-mkl
  bluesky            conda-forge/noarch::bluesky-1.5.5-py_0
  boltons            conda-forge/noarch::boltons-20.1.0-pyh9f0ad1d_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/linux-64::certifi-2020.4.5.1-py38_0
  cffi               pkgs/main/linux-64::cffi-1.14.0-py38h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py38_1003
  cryptography       pkgs/main/linux-64::cryptography-2.8-py38h1ba5d50_0
  cycler             pkgs/main/linux-64::cycler-0.10.0-py38_0
  cytoolz            pkgs/main/linux-64::cytoolz-0.10.1-py38h7b6447c_0
  databroker         conda-forge/noarch::databroker-0.13.3-py_0
  dbus               pkgs/main/linux-64::dbus-1.13.14-hb2f20db_0
  decorator          pkgs/main/noarch::decorator-4.4.2-py_0
  doct               conda-forge/noarch::doct-1.1.0-py_0
  epics-base         conda-forge/linux-64::epics-base-7.0.3.1-h68659b9_2
  epicscorelibs      conda-forge/linux-64::epicscorelibs-7.0.3.99.2.0-py38h68659b9_0
  event-model        conda-forge/noarch::event-model-1.15.0-py_0
  expat              pkgs/main/linux-64::expat-2.2.6-he6710b0_0
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0
  freetype           pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
  glib               pkgs/main/linux-64::glib-2.63.1-h5a9c865_0
  gst-plugins-base   pkgs/main/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
  gstreamer          pkgs/main/linux-64::gstreamer-1.14.0-hb453b48_1
  h5py               pkgs/main/linux-64::h5py-2.10.0-py38h7918eee_0
  hdf5               pkgs/main/linux-64::hdf5-1.10.4-hb1b8bf9_0
  historydict        conda-forge/noarch::historydict-1.2.3-py_0
  humanize           pkgs/main/noarch::humanize-0.5.1-py_1
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3
  idna               pkgs/main/noarch::idna-2.9-py_1
  importlib_metadata pkgs/main/linux-64::importlib_metadata-1.5.0-py38_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2020.0-166
  ipython            pkgs/main/linux-64::ipython-7.13.0-py38h5ca1d4c_0
  ipython_genutils   pkgs/main/linux-64::ipython_genutils-0.2.0-py38_0
  jedi               pkgs/main/linux-64::jedi-0.17.0-py38_0
  jinja2             pkgs/main/noarch::jinja2-2.11.2-py_0
  jpeg               pkgs/main/linux-64::jpeg-9b-h024ee3a_2
  jsonschema         pkgs/main/linux-64::jsonschema-3.2.0-py38_0
  kiwisolver         pkgs/main/linux-64::kiwisolver-1.2.0-py38hfd86e86_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libsodium          pkgs/main/linux-64::libsodium-1.0.16-h1bed415_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  libtiff            pkgs/main/linux-64::libtiff-4.1.0-h2733197_0
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             pkgs/main/linux-64::libxcb-1.13-h1bed415_1
  libxml2            pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1
  libxslt            pkgs/main/linux-64::libxslt-1.1.33-h7d1a2b0_0
  lmfit              conda-forge/noarch::lmfit-1.0.0-py_0
  lxml               pkgs/main/linux-64::lxml-4.5.0-py38hefd8a0e_0
  markupsafe         pkgs/main/linux-64::markupsafe-1.1.1-py38h7b6447c_0
  matplotlib         pkgs/main/linux-64::matplotlib-3.1.3-py38_0
  matplotlib-base    pkgs/main/linux-64::matplotlib-base-3.1.3-py38hef1b27d_0
  mkl                pkgs/main/linux-64::mkl-2020.0-166
  mkl-service        pkgs/main/linux-64::mkl-service-2.3.0-py38he904b0f_0
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.0.15-py38ha843d7b_0
  mkl_random         pkgs/main/linux-64::mkl_random-1.1.0-py38h962f231_0
  mongoquery         conda-forge/noarch::mongoquery-1.3.5-py_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  networkx           pkgs/main/noarch::networkx-2.4-py_0
  numpy              pkgs/main/linux-64::numpy-1.18.1-py38h4f9e942_0
  numpy-base         pkgs/main/linux-64::numpy-base-1.18.1-py38hde5b4d6_1
  olefile            pkgs/main/noarch::olefile-0.46-py_0
  openssl            pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
  ophyd              nsls2forge/noarch::ophyd-1.4.0rc3-py_0
  pandas             pkgs/main/linux-64::pandas-1.0.3-py38h0573a6f_0
  parso              pkgs/main/noarch::parso-0.7.0-py_0
  pcre               pkgs/main/linux-64::pcre-8.43-he6710b0_0
  perl               pkgs/main/linux-64::perl-5.26.2-h14c3975_0
  pexpect            pkgs/main/linux-64::pexpect-4.8.0-py38_0
  pickleshare        pkgs/main/linux-64::pickleshare-0.7.5-py38_1000
  pillow             pkgs/main/linux-64::pillow-7.1.2-py38hb39fc2d_0
  pims               pkgs/main/noarch::pims-0.4.1-py_1
  pip                pkgs/main/linux-64::pip-20.0.2-py38_1
  prettytable        conda-forge/noarch::prettytable-0.7.2-py_3
  prompt-toolkit     pkgs/main/noarch::prompt-toolkit-3.0.4-py_0
  prompt_toolkit     pkgs/main/noarch::prompt_toolkit-3.0.4-0
  ptyprocess         pkgs/main/linux-64::ptyprocess-0.6.0-py38_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_0
  pyepics            conda-forge/linux-64::pyepics-3.4.1-py38_0
  pygments           pkgs/main/noarch::pygments-2.6.1-py_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py38_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.7-py_0
  pyqt               pkgs/main/linux-64::pyqt-5.9.2-py38h05f1152_4
  pyresttable        aps-anl-tag/noarch::pyresttable-2020.0.2-py_0
  pyrsistent         pkgs/main/linux-64::pyrsistent-0.16.0-py38h7b6447c_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py38_0
  python             pkgs/main/linux-64::python-3.8.2-hcf32534_0
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-py_0
  pytz               pkgs/main/noarch::pytz-2020.1-py_0
  pyyaml             pkgs/main/linux-64::pyyaml-5.3.1-py38h7b6447c_0
  pyzmq              pkgs/main/linux-64::pyzmq-18.1.1-py38he6710b0_0
  qt                 pkgs/main/linux-64::qt-5.9.7-h5867ecd_1
  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0
  requests           pkgs/main/linux-64::requests-2.23.0-py38_0
  scipy              pkgs/main/linux-64::scipy-1.4.1-py38h0b6359f_0
  setuptools         pkgs/main/linux-64::setuptools-46.1.3-py38_0
  sip                pkgs/main/linux-64::sip-4.19.13-py38he6710b0_0
  six                pkgs/main/linux-64::six-1.14.0-py38_0
  slicerator         pkgs/main/noarch::slicerator-1.0.0-py_0
  spec2nexus         aps-anl-tag/noarch::spec2nexus-2021.1.7-h39e3cac_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
  super_state_machi~ conda-forge/noarch::super_state_machine-2.0.2-py_0
  tifffile           pkgs/main/linux-64::tifffile-0.15.1-py38heb32a55_2
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  toolz              pkgs/main/noarch::toolz-0.10.0-py_0
  tornado            pkgs/main/linux-64::tornado-6.0.4-py38h7b6447c_1
  tqdm               pkgs/main/noarch::tqdm-4.46.0-py_0
  traitlets          pkgs/main/linux-64::traitlets-4.3.3-py38_0
  tzlocal            pkgs/main/linux-64::tzlocal-2.0.0-py38_0
  ujson              pkgs/main/linux-64::ujson-2.0.3-py38he6710b0_0
  uncertainties      conda-forge/linux-64::uncertainties-3.1.2-py38_0
  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py38_0
  wcwidth            pkgs/main/noarch::wcwidth-0.1.9-py_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py38_0
  xlrd               pkgs/main/noarch::xlrd-1.2.0-py_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zeromq             pkgs/main/linux-64::zeromq-4.3.1-he6710b0_3
  zipp               pkgs/main/noarch::zipp-3.1.0-py_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
  zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0

Good, somewhat. apstools version as requested, but spec2nexus is less than latest available: 2021.1.7

prjemian · 2020-05-07T16:45:33Z

Apply restrictions on other requirements as well. Also, pymongo only needed for the snapshot gui so dropping it from the list at least for now.

prjemian · 2020-05-07T16:58:17Z

now:

conda create -n apstools "apstools=1.2.3rc3" -c defaults -c conda-forge -c aps-anl-tag -c nsls2forge  2>&1 | tee /tmp/install.txt

prjemian · 2020-05-07T17:01:18Z

Not yet: Among other items, databroker is wrong version:

  databroker         conda-forge/noarch::databroker-0.13.3-py_0

The requirements.txt file is for pip and conda build. Need to also update the meta.yaml file.

prjemian · 2020-05-07T19:00:44Z

But this won't conda build due to missing packages. Particularly needed the lightsource2-tag channel. Added that to the linux account's conda channel list $HOME/.condarc and this builds and uploads now. Here's my channel list:

channels:
  - defaults
  - conda-forge
  - nsls2forge
  - aps-anl-tag
  - aps-anl-dev
  - prjemian
  - lightsource2-tag
  - lightsource2-dev
  - pydm-tag
  - pydm-dev
  - pcds-tag
  - pcds-dev

prjemian · 2020-05-07T19:08:18Z

Solved!

prjemian added the task Something to be done. label May 7, 2020

prjemian added this to the 1.2.3 milestone May 7, 2020

prjemian self-assigned this May 7, 2020

prjemian added a commit that referenced this issue May 7, 2020

MNT #313 rebuild by code examination

96d890e

prjemian added a commit that referenced this issue May 7, 2020

MNT #313 remove standard library packages from requirements

7ad34ed

prjemian added a commit that referenced this issue May 7, 2020

MNT #313

58a6efa

prjemian added a commit that referenced this issue May 7, 2020

MNT #313 conda requirements

7788550

prjemian closed this as completed May 7, 2020

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

update packaging requirements #313

update packaging requirements #313

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020 •

edited

Loading

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

update packaging requirements #313

update packaging requirements #313

Comments

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020 • edited Loading

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020

prjemian commented May 7, 2020 •

edited

Loading