Cannot run tutorial after active papers installation

[sjdv1982]

Active papers installation

Environment

active_papers.yml

name: active-papers
channels:
 - conda-forge
dependencies:
 - python=3.5
 - pip
 - h5py>=2.2
 - numpy>=1.6
 - pip:
 - tempdir>=0.6
 - matplotlib

Installation commands

mamba env create --file active-papers.yml
conda activate active-papers
git clone https://github.com/activepapers/activepapers-python
cd activepapers-python
python3 setup.py install

Installed packages

conda list

Output:

# packages in environment at /home/sjoerd/miniconda3/envs/active-papers:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
activepapers-py 0.2.2 pypi_0 pypi
blas 1.1 openblas conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
certifi 2018.8.24 py35_1001 conda-forge
cycler 0.10.0 pypi_0 pypi
h5py 2.8.0 py35h7eb728f_2 conda-forge
hdf5 1.10.2 hc401514_3 conda-forge
kiwisolver 1.1.0 pypi_0 pypi
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran 3.0.0 1 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
matplotlib 3.0.3 pypi_0 pypi
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.15.2 py35_blas_openblashd3ea46f_0 conda-forge
openblas 0.2.20 8 conda-forge
openssl 1.0.2u h516909a_0 conda-forge
pip 20.3.4 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pypi_0 pypi
python 3.5.5 h5001a0f_2 conda-forge
python-dateutil 2.8.2 pypi_0 pypi
readline 7.0 hf8c457e_1001 conda-forge
setuptools 40.4.3 py35_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.28.0 h8b20d00_0 conda-forge
tempdir 0.7.1 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge

Running the tutorial

aptool checkout data

Output:

Skipping /data/correlation_function_integration_limit: data type data not extractable
Skipping /data/correlation_function_plot_range: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_1: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_10: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_2: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_3: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_4: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_5: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_6: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_7: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_8: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_9: data type data not extractable
Skipping /data/correlation_functions/correlation_function_laboratory_frame_averaged: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_1: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_10: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_2: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_3: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_4: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_5: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_6: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_7: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_8: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_9: data type data not extractable
Skipping /data/correlation_functions/correlation_function_molecular_frame_averaged: data type data not extractable
Skipping /data/correlation_functions/correlation_function_time: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_1: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_10: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_2: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_3: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_4: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_5: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_6: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_7: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_8: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_9: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_laboratory_frame_averaged: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_1: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_10: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_2: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_3: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_4: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_5: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_6: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_7: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_8: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_9: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_molecular_frame_averaged: data type data not extractable
Skipping /data/correlation_functions/mean_square_displacement_time: data type data not extractable
Skipping /data/diffusion_tensor_kubo_laboratory_frame: data type data not extractable
Skipping /data/diffusion_tensor_kubo_molecular_frame: data type data not extractable
Skipping /data/diffusion_tensor_msd_laboratory_frame: data type data not extractable
Skipping /data/diffusion_tensor_msd_molecular_frame: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_1: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_10: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_2: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_3: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_4: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_5: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_6: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_7: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_8: data type data not extractable
Skipping /data/mass_and_inertia/inertia_tensor_9: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_1: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_10: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_2: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_3: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_4: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_5: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_6: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_7: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_8: data type data not extractable
Skipping /data/mass_and_inertia/reduced_mass_9: data type data not extractable
Skipping /data/msd_fit_range: data type data not extractable
Skipping /data/msd_plot_range: data type data not extractable
Skipping /data/reference_structures/reference_structure_1/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_1/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_1/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_10/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_10/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_10/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_2/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_2/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_2/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_3/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_3/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_3/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_4/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_4/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_4/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_5/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_5/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_5/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_6/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_6/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_6/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_7/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_7/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_7/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_8/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_8/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_8/universe: data type data not extractable
Skipping /data/reference_structures/reference_structure_9/atom_masses: data type data not extractable
Skipping /data/reference_structures/reference_structure_9/configuration: data type data not extractable
Skipping /data/reference_structures/reference_structure_9/universe: data type data not extractable
Skipping /data/temperature: data type data not extractable
Skipping /data/thermal_velocities/variance_angular_velocity_laboratory_frame: data type data not extractable
Skipping /data/thermal_velocities/variance_angular_velocity_molecular_frame: data type data not extractable
Skipping /data/thermal_velocities/variance_velocity_laboratory_frame: data type data not extractable
Skipping /data/thermal_velocities/variance_velocity_molecular_frame: data type data not extractable
Skipping /data/trajectory/center_of_mass_1: data type data not extractable
Skipping /data/trajectory/center_of_mass_10: data type data not extractable
Skipping /data/trajectory/center_of_mass_2: data type data not extractable
Skipping /data/trajectory/center_of_mass_3: data type data not extractable
Skipping /data/trajectory/center_of_mass_4: data type data not extractable
Skipping /data/trajectory/center_of_mass_5: data type data not extractable
Skipping /data/trajectory/center_of_mass_6: data type data not extractable
Skipping /data/trajectory/center_of_mass_7: data type data not extractable
Skipping /data/trajectory/center_of_mass_8: data type data not extractable
Skipping /data/trajectory/center_of_mass_9: data type data not extractable
Skipping /data/trajectory/orientation_1: data type data not extractable
Skipping /data/trajectory/orientation_10: data type data not extractable
Skipping /data/trajectory/orientation_2: data type data not extractable
Skipping /data/trajectory/orientation_3: data type data not extractable
Skipping /data/trajectory/orientation_4: data type data not extractable
Skipping /data/trajectory/orientation_5: data type data not extractable
Skipping /data/trajectory/orientation_6: data type data not extractable
Skipping /data/trajectory/orientation_7: data type data not extractable
Skipping /data/trajectory/orientation_8: data type data not extractable
Skipping /data/trajectory/orientation_9: data type data not extractable
Skipping /data/trajectory/time: data type data not extractable
Skipping /data/trajectory_suffixes: data type data not extractable

ls -l `find data -type f -name '*'`

Output:

-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_function_integration_limit
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_function_plot_range
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_laboratory_frame_averaged
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_molecular_frame_averaged
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/correlation_function_time
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_laboratory_frame_averaged
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_molecular_frame_averaged
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/correlation_functions/mean_square_displacement_time
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/diffusion_tensor_kubo_laboratory_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/diffusion_tensor_kubo_molecular_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/diffusion_tensor_msd_laboratory_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/diffusion_tensor_msd_molecular_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/inertia_tensor_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/mass_and_inertia/reduced_mass_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/msd_fit_range
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/msd_plot_range
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_1/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_1/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_1/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_10/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_10/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_10/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_2/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_2/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_2/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_3/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_3/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_3/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_4/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_4/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_4/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_5/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_5/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_5/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_6/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_6/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_6/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_7/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_7/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_7/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_8/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_8/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_8/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_9/atom_masses
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_9/configuration
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/reference_structures/reference_structure_9/universe
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/temperature
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/thermal_velocities/variance_angular_velocity_laboratory_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/thermal_velocities/variance_angular_velocity_molecular_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/thermal_velocities/variance_velocity_laboratory_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/thermal_velocities/variance_velocity_molecular_frame
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/center_of_mass_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_1
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_10
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_2
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_3
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_4
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_5
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_6
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_7
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_8
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/orientation_9
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory/time
-rw-rw-r-- 1 sjoerd sjoerd 0 Feb 3 16:07 data/trajectory_suffixes

aptool update -v

Traceback (most recent call last):
 File "/home/sjoerd/miniconda3/envs/active-papers/bin/aptool", line 4, in <module>
 __import__('pkg_resources').run_script('ActivePapers.Py==0.2.2', 'aptool')
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/pkg_resources/__init__.py", line 661, in run_script
 self.require(requires)[0].run_script(script_name, ns)
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1441, in run_script
 exec(code, namespace, namespace)
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/EGG-INFO/scripts/aptool", line 258, in <module>
 func(**args)
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/activepapers/cli.py", line 424, in update
 calclet, item_name = _find_calclet_for_dummy_or_stale_item(paper_name)
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/activepapers/cli.py", line 403, in _find_calclet_for_dummy_or_stale_item
 next(deps) # the first set has no dependencies
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/activepapers/storage.py", line 483, in dependency_hierarchy
 frozenset(dep.name for dep in self.iter_dependencies(item)))
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/activepapers/storage.py", line 483, in <genexpr>
 frozenset(dep.name for dep in self.iter_dependencies(item)))
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/ActivePapers.Py-0.2.2-py3.5.egg/activepapers/storage.py", line 418, in iter_dependencies
 yield self.file[dep]
 File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
 File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.5/site-packages/h5py/_hl/group.py", line 177, in __getitem__
 oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
 File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
 File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
 File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: 'Unable to open object (component not found)'

[khinsen]

The "data not extractable" messages are expected. "aptool checkout" is meant for code and documentation, and can in fact only handle text. Anything labelled "data" is an HDF5 dataset. It doesn't have an obvious on-disk representation that could be checked out.

Accessing the data thus requires HDF5. The ActivePaper file is an HDF5 file, so you can open it using h5py and simply access all the datasets.

[khinsen]

Nevertheless, aptool update -v should work, and it does on my machine. It generates lots of warnings from matplotlib, plus one from Python, which are due to Python and matplotlib having evolved in the meantime (neither caring much about backwards compatibility). Here is the complete output I get:

~/Temp/ap-tutorial $ guix shell python python-activepapers python-matplotlib -- aptool update -v
Dataset /data/coordinate_trajectories/translation_molecular_frame_9 is stale or dummy, running /code/trajectory_processing
Dataset /data/correlation_functions/mean_square_displacement_molecular_frame_8 is stale or dummy, running /code/correlation_functions
Dataset /documentation/msd_rr_off_diagonal.pdf is stale or dummy, running /code/plots
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'x' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'y' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'z' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'x' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'y' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'z' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'x' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'y' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'z' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'x' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'y' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'z' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'xz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'yz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zx' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zy' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
7f13f833dd00:/code/plots:24: UserWarning: Legend does not support 'zz' instances.
A proxy artist may be used instead.
See: https://matplotlib.org/users/legend_guide.html#creating-artists-specifically-for-adding-to-the-legend-aka-proxy-artists
Dataset /data/diffusion_tensor_msd_laboratory_frame is stale or dummy, running /code/diffusion_tensor
7f13ee3f7fd0:/code/python-packages/fitting:9: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.

[khinsen]

So the big question is: what's different between our environments? Guix has 214 dependencies of ActivePapers, but that's because it includes all compile-time tools, recursively. Picking from that list the packages you have listed above, as much as possible, I find:

python-activepapers@0.2.2
bzip2@1.0.8
python-h5py@3.6.0
hdf5@1.10.7
libffi@3.3
gfortran@10.3.0
libstdc++@10.3.0
zlib@1.2.11
python-matplotlib@3.5.2
ncurses@6.2.20210619
python-numpy@1.21.6
openblas@0.3.20
openssl@1.1.1l
python-pyparsing@3.0.6
python@3.9.9
readline@8.1.1
python-six@1.16.0
sqlite@3.36.0
python-tempdir@0.7.1
tk@8.6.11.1
python-wheel@0.37.0
xz@5.2.5
zlib@1.2.11

Lots of small differences, nothing that looks obviously problematic.

[khinsen]

Looking at your traceback, what strikes me is the file name ActivePapers.Py-0.1.4-py3.5.egg, in an environment claiming to contain ActivePapers 0.2.2. There are more than three years between 0.1.4 and 0.2.2.

Could you check what the file `activepapers/version.py' contains in your environment?

[sjdv1982]

Looking at your traceback, what strikes me is the file name ActivePapers.Py-0.1.4-py3.5.egg, in an environment claiming to contain ActivePapers 0.2.2. There are more than three years between 0.1.4 and 0.2.2.

Could you check what the file `activepapers/version.py' contains in your environment?

Ah, I also tried the PyPI ActivePapers version, and I copy-pasted the wrong traceback. Now edited. But it doesn't look different.

The "data not extractable" messages are expected. "aptool checkout" is meant for code and documentation, and can in fact only handle text. Anything labelled "data" is an HDF5 dataset. It doesn't have an obvious on-disk representation that could be checked out.

What I would expect is either:

• The error message above ("aptool checkout" is meant for code and documentation...)
• Data files written out in .npy format

A list of zero-byte files is not what I expected.

Accessing the data thus requires HDF5. The ActivePaper file is an HDF5 file, so you can open it using h5py and simply access all the datasets.

It's a bit scary to have scientific data hidden from non-programmers. If you wish, I could cook up an extract data script that does the equivalent of tar -xf lysozyme.ap

[sjdv1982]

So the big question is: what's different between our environments? Guix has 214 dependencies of ActivePapers, but that's because it includes all compile-time tools, recursively. Picking from that list the packages you have listed above, as much as possible, I find:

python-activepapers@0.2.2
bzip2@1.0.8
python-h5py@3.6.0
hdf5@1.10.7
libffi@3.3
gfortran@10.3.0
libstdc++@10.3.0
zlib@1.2.11
python-matplotlib@3.5.2
ncurses@6.2.20210619
python-numpy@1.21.6
openblas@0.3.20
openssl@1.1.1l
python-pyparsing@3.0.6
python@3.9.9
readline@8.1.1
python-six@1.16.0
sqlite@3.36.0
python-tempdir@0.7.1
tk@8.6.11.1
python-wheel@0.37.0
xz@5.2.5
zlib@1.2.11

Lots of small differences, nothing that looks obviously problematic.

This is the best I can do in order to match your package versions:

name: active-papers
channels:
 - conda-forge
dependencies:
 - python=3.9
 - pip
 - hdf5=1.10
 - numpy==1.21
 - pip:
 - h5py==3.6.*
 - tempdir==0.7.*
 - matplotlib

No difference in the traceback

 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.9/site-packages/ActivePapers.Py-0.2.2-py3.9.egg/activepapers/storage.py", line 418, in iter_dependencies
 yield self.file[dep]
 File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
 File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
 File "/home/sjoerd/miniconda3/envs/active-papers/lib/python3.9/site-packages/h5py/_hl/group.py", line 305, in __getitem__
 oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
 File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
 File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
 File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: 'Unable to open object (component not found)'

EDIT: better matching of the package versions

[khinsen]

I agree about data checkout, and opened an issue for that (#21).

Thanks for trying to match my versions! This still looks weird. I'll have to debug this under Miniconda.