openpathsampling/ops_tutorial

Introductory tutorial on TPS, committor analysis, and (MS)TIS with OpenPathSampling

OpenPathSampling

An open source Python framework for transition interface and path sampling calculations.

See documentation here:

http://openpathsampling.org

ops_tutorial's Issues

Update tutorial to use "hooks"

As of OpenPathSampling 1.5, the best way to get certain custom behavior is with "hooks." In particular, this affects the live visualizer in notebook 4. The tutorials should be updated to use the current best practices.

Feedback from MolSim 2021

A few points that came up in discussions, mostly with the TAs, from MolSim 2021 as to ways to improve the tutorial. The main theme is that there are a lot of places where the student is to answer some question, but no context is provided for why that question is something you might want to look at.

For all notebooks:

• Make sure that axes are labelled in plots
• Possibly recommend installing requirements via the conda env used by binder [EDIT: This was because, at the time, OpenMM didn't work on Python 3.8 or 3.9. Now that OpenMM is on conda-forge, this is not a problem.]

From notebook 2:

• What is the significance of getting both forward and backward paths?
• Why do we care about number of steps between decorrelated trajectories?
• Why might you visualize the shooting points?
• Better explain significance of fixed-length vs. flexible-length TPS
• Maybe clarify that there are many paths that switch channels (in the path density)
• Fix grammar on last sentence of the notebook

From notebook 3:

• Clarify the need for full equivalence, i.e., must show that both q=q* => p_B(q)=1/2 and p_B(q)=1/2 => q=q*.

Feedback from MolSSI school tutorial (June 2021)

This is a list of improvements to make that came from the OPS tutorial we held as a satellite event to the Virtual MolSSI School on Open Source Software for Rare Event Sampling Strategies.

Several of these will actually involve making improvements in the OPS docs, rather than making significant changes to the text here.

• Replace link to builder.openmm.org with link to openmm-setup app (#18)
• Add links to the OPS website as a way to get other examples
• Create more detailed discussion of path tree (on OPS website), link to that

(This will be update as we get more feedback.)

Biased simulation in tutorial 5 seems broken

I am running through these notebooks with a new environment.

When I try to run the:
openpathsampling pathsampling shooting_setup.nc -o biased.nc --scheme biased_shooting -n 500 command the code seems to be unable to collect the engine object (this is not an issue in the regular simulation from the same file)

The code errors out in either the backward partial

stack trace

Working on Monte Carlo cycle number 1
Starting simulation...
Working on first step
Traceback (most recent call last):
  File "/home/sroet/miniconda3/envs/ops/bin/openpathsampling", line 33, in <module>
    sys.exit(load_entry_point('openpathsampling-cli', 'console_scripts', 'openpathsampling')())
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1137, in __call__
    return self.main(*args, **kwargs)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1062, in main
    rv = self.invoke(ctx)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 763, in invoke
    return __callback(*args, **kwargs)
  File "/home/sroet/github_files/openpathsampling-cli/paths_cli/commands/pathsampling.py", line 22, in pathsampling
    pathsampling_main(output_storage=OUTPUT_FILE.get(output_file),
  File "/home/sroet/github_files/openpathsampling-cli/paths_cli/commands/pathsampling.py", line 35, in pathsampling_main
    simulation.run(n_steps)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathsimulators/path_sampling.py", line 261, in run
    hook_state, mcstep = self.run_one_step(step_info, hook_state)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathsimulators/path_sampling.py", line 291, in run_one_step
    movepath = self._mover.move(self.sample_set, step=self.step)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2594, in move
    self.mover.move(sample_set),
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 615, in move
    change = self.move_core(samples)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 642, in move_core
    trials, call_details = self(*samples)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 787, in __call__
    trial_trajectory, run_details = self._run(initial_trajectory,
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2365, in _run
    bkwd_partial = self._make_backward_trajectory(trajectory, modified,
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2284, in _make_backward_trajectory
    bkwd_partial = self.engine.generate(initial_snapshot.reversed,
AttributeError: 'NoneType' object has no attribute 'generate'
AttributeError: __getattribute__
Exception ignored in: 'netCDF4._netCDF4.Dataset.__dealloc__'
AttributeError: __getattribute__
AttributeError: __getattribute__
Exception ignored in: 'netCDF4._netCDF4.Dataset.__dealloc__'
AttributeError: __getattribute__

or the forward partial:

stack trace

Working on Monte Carlo cycle number 1
Starting simulation...
Working on first step
Traceback (most recent call last):
  File "/home/sroet/miniconda3/envs/ops/bin/openpathsampling", line 33, in <module>
    sys.exit(load_entry_point('openpathsampling-cli', 'console_scripts', 'openpathsampling')())
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1137, in __call__
    return self.main(*args, **kwargs)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1062, in main
    rv = self.invoke(ctx)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/sroet/miniconda3/envs/ops/lib/python3.9/site-packages/click/core.py", line 763, in invoke
    return __callback(*args, **kwargs)
  File "/home/sroet/github_files/openpathsampling-cli/paths_cli/commands/pathsampling.py", line 22, in pathsampling
    pathsampling_main(output_storage=OUTPUT_FILE.get(output_file),
  File "/home/sroet/github_files/openpathsampling-cli/paths_cli/commands/pathsampling.py", line 35, in pathsampling_main
    simulation.run(n_steps)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathsimulators/path_sampling.py", line 261, in run
    hook_state, mcstep = self.run_one_step(step_info, hook_state)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathsimulators/path_sampling.py", line 291, in run_one_step
    movepath = self._mover.move(self.sample_set, step=self.step)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2594, in move
    self.mover.move(sample_set),
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 1575, in move
    subchange = mover.move(sample_set)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 615, in move
    change = self.move_core(samples)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 642, in move_core
    trials, call_details = self(*samples)
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 787, in __call__
    trial_trajectory, run_details = self._run(initial_trajectory,
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2321, in _run
    fwd_partial = self._make_forward_trajectory(trajectory, modified,
  File "/home/sroet/github_files/openpathsampling/openpathsampling/pathmover.py", line 2273, in _make_forward_trajectory
    fwd_partial = self.engine.generate(initial_snapshot,
AttributeError: 'NoneType' object has no attribute 'generate'
AttributeError: __getattribute__
Exception ignored in: 'netCDF4._netCDF4.Dataset.__dealloc__'
AttributeError: __getattribute__
AttributeError: __getattribute__
Exception ignored in: 'netCDF4._netCDF4.Dataset.__dealloc__'
AttributeError: __getattribute__

With a bunch of netcdf errors.

I run with the current conda setup:

conda list

# packages in environment at /home/sroet/miniconda3/envs/ops:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
argon2-cffi               20.1.0           py39h3811e60_2    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.2.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bhmm                      0.6.3           py39h16ac069_1004    conda-forge
bleach                    4.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
cffi                      1.14.6           py39he32792d_0    conda-forge
cftime                    1.5.0            py39hce5d2b2_0    conda-forge
click                     8.0.1            py39hf3d152e_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
coverage                  5.5              py39h3811e60_0    conda-forge
cudatoolkit               11.2.2               he111cf0_8    conda-forge
curl                      7.78.0               hea6ffbf_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
debugpy                   1.4.1            py39he80948d_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
deeptime                  0.2.9            py39hde0f152_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.4              pyhd8ed1ab_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
fftw                      3.3.9           nompi_h74d3f13_101    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2           py39hf3d152e_3    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
glib                      2.68.3               h9c3ff4c_0    conda-forge
glib-tools                2.68.3               h9c3ff4c_0    conda-forge
greenlet                  1.1.1            py39he80948d_0    conda-forge
gst-plugins-base          1.18.4               hf529b03_2    conda-forge
gstreamer                 1.18.4               h76c114f_2    conda-forge
h5py                      3.3.0           nompi_py39h98ba4bc_100    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
importlib-metadata        4.6.4            py39hf3d152e_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
ipykernel                 6.1.0            py39hef51801_0    conda-forge
ipython                   7.26.0           py39hef51801_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.3              pyhd3deb0d_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.0           py39hf3d152e_2    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter                   1.0.0            py39hf3d152e_6    conda-forge
jupyter_client            6.1.12             pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.7.1            py39hf3d152e_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.0              pyhd8ed1ab_1    conda-forge
kiwisolver                1.3.1            py39h1a9c180_1    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcurl                   7.78.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               hcdb4288_3    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.1.0               hc902ee8_8    conda-forge
libgfortran-ng            11.1.0               h69a702a_8    conda-forge
libgfortran5              11.1.0               h6c583b3_8    conda-forge
libglib                   2.68.3               h3e27bee_0    conda-forge
libgomp                   11.1.0               hc902ee8_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm11                 11.1.0               hf817b99_2    conda-forge
libnetcdf                 4.8.0           nompi_hcd642e3_103    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     13.3                 hd57d9b9_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              11.1.0               h56837e0_8    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libzip                    1.8.0                h4de3113_0    conda-forge
llvmlite                  0.36.0           py39h1bbdace_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.0.1            py39h3811e60_0    conda-forge
matplotlib                3.4.3            py39hf3d152e_0    conda-forge
matplotlib-base           3.4.3            py39h2fa2bec_0    conda-forge
matplotlib-inline         0.1.2              pyhd8ed1ab_2    conda-forge
mdtraj                    1.9.6            py39h138c130_1    conda-forge
mistune                   0.8.4           py39h3811e60_1004    conda-forge
mock                      4.0.3            py39hf3d152e_1    conda-forge
more-itertools            8.8.0              pyhd8ed1ab_0    conda-forge
mpiplus                   v0.0.1          py39hde42818_1002    conda-forge
msmtools                  1.2.6            py39hce5d2b2_0    conda-forge
multiprocess              0.70.12.2        py39h3811e60_0    conda-forge
mysql-common              8.0.25               ha770c72_2    conda-forge
mysql-libs                8.0.25               hfa10184_2    conda-forge
nbclient                  0.5.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.1.0            py39hf3d152e_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
nbval                     0.9.6              pyh9f0ad1d_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
nest-asyncio              1.5.1              pyhd8ed1ab_0    conda-forge
netcdf4                   1.5.7           nompi_py39hc6dca20_100    conda-forge
networkx                  2.6.2              pyhd8ed1ab_0    conda-forge
nglview                   3.0.3              pyh8a188c0_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  6.4.3              pyha770c72_0    conda-forge
nspr                      4.30                 h9c3ff4c_0    conda-forge
nss                       3.69                 hb5efdd6_0    conda-forge
numba                     0.53.1           py39h56b8d98_1    conda-forge
numexpr                   2.7.3            py39hde0f152_0    conda-forge
numpy                     1.21.1           py39hdbf815f_0    conda-forge
ocl-icd                   2.3.0                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmm                    7.5.1            py39h71eca04_1    conda-forge
openmmtools               0.20.3             pyhd8ed1ab_0    conda-forge
openpathsampling          1.5.2.dev0                dev_0    <develop>
openpathsampling-cli      0.2.2.dev0                dev_0    <develop>
openssl                   1.1.1k               h7f98852_0    conda-forge
packaging                 21.0               pyhd8ed1ab_0    conda-forge
pandas                    1.3.1            py39hde0f152_0    conda-forge
pandoc                    2.14.1               h7f98852_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.8.2              pyhd8ed1ab_0    conda-forge
pathos                    0.2.8              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pdbfixer                  1.7                pyhd3deb0d_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.3.1            py39ha612740_0    conda-forge
pip                       21.2.4             pyhd8ed1ab_0    conda-forge
pluggy                    0.13.1           py39hf3d152e_4    conda-forge
pox                       0.3.0              pyhd8ed1ab_0    conda-forge
ppft                      1.6.6.4            pyhd8ed1ab_0    conda-forge
prometheus_client         0.11.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.19             pyha770c72_0    conda-forge
prompt_toolkit            3.0.19               hd8ed1ab_0    conda-forge
psutil                    5.8.0            py39h3811e60_1    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyemma                    2.5.9            py39hde0f152_0    conda-forge
pygments                  2.9.0              pyhd8ed1ab_0    conda-forge
pymbar                    3.0.5            py39hce5d2b2_2    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py39hf3d152e_7    conda-forge
pyqt-impl                 5.12.3           py39h0fcd23e_7    conda-forge
pyqt5-sip                 4.19.18          py39he80948d_7    conda-forge
pyqtchart                 5.12             py39h0fcd23e_7    conda-forge
pyqtwebengine             5.12.1           py39h0fcd23e_7    conda-forge
pyrsistent                0.17.3           py39h3811e60_2    conda-forge
pytables                  3.6.1            py39hf6dc253_3    conda-forge
pytest                    6.2.4            py39hf3d152e_0    conda-forge
python                    3.9.6           h49503c6_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py39h3811e60_0    conda-forge
pyzmq                     22.2.1           py39h37b5a0c_0    conda-forge
qt                        5.12.9               hda022c4_4    conda-forge
qtconsole                 5.1.1              pyhd8ed1ab_0    conda-forge
qtpy                      1.9.0                      py_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
scikit-learn              0.24.2           py39h4dfa638_1    conda-forge
scipy                     1.7.1            py39hee8e79c_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                49.6.0           py39hf3d152e_3    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.8                he1b5a44_3    conda-forge
sqlalchemy                1.4.22           py39h3811e60_0    conda-forge
sqlite                    3.36.0               h9cd32fc_0    conda-forge
svgwrite                  1.4.1              pyhd8ed1ab_0    conda-forge
terminado                 0.10.1           py39hf3d152e_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             2.2.0              pyh8a188c0_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
tqdm                      4.62.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
ujson                     4.0.2            py39he80948d_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.0             pyhd8ed1ab_1    conda-forge
widgetsnbextension        3.5.1            py39hf3d152e_4    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h516909a_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_0    conda-forge
zipp                      3.5.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge