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#3750 closed defect (fixed)

Bundle builder: DataDir from extra package not copied

Reported by:	tony.schaefer@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Build System	Version:
Keywords:		Cc:	chimera-programmers, Tristan Croll
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I'm having issues with the <DataFiles> section in my bundle_info (I might just not be following the documentation well enough). I can get `devel build` to find a DataFile for an additional package, but not a DataDir. Relevant bundle_info.xml snippet:

```xml
    <AdditionalPackages>
        <Package name="AaronTools" folder="../AaronTools-distro">
        </Package>
    </AdditionalPackages>

    <DataFiles package="AaronTools">
        <DataDir>Ligands</DataDir>
        <DataDir>Substituents</DataDir>
        <DataDir>Rings</DataDir>
        <DataDir>utils</DataDir>
        <DataFile>bond_data.json</DataFile>
        <DataFile>calculated_bond_lengths.json</DataFile>
        <DataFile>README.md</DataFile>
        <DataFile>LICENSE</DataFile>
    </DataFiles>
```

The file structure of the AaronTools-distro folder is:
Ligands/xyz files
Rings/xyz files
Substituents/xyz files
theory/__init__.py, other .py files
utils/.py files
LICENSE
bond_data.json
calculated_bond_lengths.json
README.md
__init__.py
(other .py files)

For this AaronTools-distro setup, `devel build` will add the ExtraFile's to the AaronTools package, but not the ExtraDir's. I've tried moving these files and directories to AaronTools-distro/src (the documentation on bundle_info.xml says they should be in a directory named "src"), but then `devel build` can't find any ExtraFile's or ExtraDir's. When building with "src" in AaronTools-distro. It also puts everything in "AaronTools/src" instead of "AaronTools". I have also tried using an absolute path instead of a relative path for the "folder" attribute of Package. I got the same results and the relative path. 

With my understanding of the documentation, I'd expect devel build to take the "Ligands", "Substituents", etc. from ../AaronTools-distro/src and copy them to AaronTools/Ligands, etc when building the bundle. 

I will note that the _expand_datafiles method of the BundleBuilder class does not utilize the "folder" package attribute. If the issue is not just my understanding of the documentation, it's probably tied to the os.walk() in this subroutine starting in my current working directory and not the additional package's folder. 

Log:
> devel clean "C:\Users\Tony Schaefer\Documents\GitHub\ChimAARON"

  

> devel build "C:\Users\Tony Schaefer\Documents\GitHub\ChimAARON"

running build  
running build_py  
creating build  
creating build\lib  
creating build\lib\SEQCROW  
copying src\io.py -> build\lib\SEQCROW  
copying src\jobs.py -> build\lib\SEQCROW  
copying src\libraries.py -> build\lib\SEQCROW  
copying src\presets.py -> build\lib\SEQCROW  
copying src\residue_collection.py -> build\lib\SEQCROW  
copying src\selectors.py -> build\lib\SEQCROW  
copying src\settings.py -> build\lib\SEQCROW  
copying src\theory.py -> build\lib\SEQCROW  
copying src\utils.py -> build\lib\SEQCROW  
copying src\\__init__.py -> build\lib\SEQCROW  
creating build\lib\SEQCROW\commands  
copying src\commands\angle.py -> build\lib\SEQCROW\commands  
copying src\commands\dihedral.py -> build\lib\SEQCROW\commands  
copying src\commands\fuseRing.py -> build\lib\SEQCROW\commands  
copying src\commands\rmsdAlign.py -> build\lib\SEQCROW\commands  
copying src\commands\substitute.py -> build\lib\SEQCROW\commands  
copying src\commands\\__init__.py -> build\lib\SEQCROW\commands  
creating build\lib\SEQCROW\managers  
copying src\managers\filereader_manager.py -> build\lib\SEQCROW\managers  
copying src\managers\job_manager.py -> build\lib\SEQCROW\managers  
copying src\managers\ordered_selection.py -> build\lib\SEQCROW\managers  
copying src\managers\\__init__.py -> build\lib\SEQCROW\managers  
creating build\lib\SEQCROW\tools  
copying src\tools\aaron_input_builder.py -> build\lib\SEQCROW\tools  
copying src\tools\browse_aarontools.py -> build\lib\SEQCROW\tools  
copying src\tools\compute_thermo.py -> build\lib\SEQCROW\tools  
copying src\tools\filereader_panel.py -> build\lib\SEQCROW\tools  
copying src\tools\input_generator.py -> build\lib\SEQCROW\tools  
copying src\tools\job_manager_tool.py -> build\lib\SEQCROW\tools  
copying src\tools\libadd.py -> build\lib\SEQCROW\tools  
copying src\tools\normal_modes.py -> build\lib\SEQCROW\tools  
copying src\tools\per_frame_plot.py -> build\lib\SEQCROW\tools  
copying src\tools\structure_editing.py -> build\lib\SEQCROW\tools  
copying src\tools\\__init__.py -> build\lib\SEQCROW\tools  
creating build\lib\SEQCROW\widgets  
copying src\widgets\comboboxes.py -> build\lib\SEQCROW\widgets  
copying src\widgets\periodic_table.py -> build\lib\SEQCROW\widgets  
copying src\widgets\\__init__.py -> build\lib\SEQCROW\widgets  
creating build\lib\AaronTools  
copying ..\AaronTools-distro\atoms.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\component.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\comp_output.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\config.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\const.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\fileIO.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\finders.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\geometry.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\job_control.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\json_extension.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\new_fileIO.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\ring.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\substituent.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\trajectory.py -> build\lib\AaronTools  
copying ..\AaronTools-distro\\__init__.py -> build\lib\AaronTools  
creating build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_atoms.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_cls.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_component.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_comp_output.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_fetch.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_fileIO.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_finders.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_geometry.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_json_extension.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_substituent.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_trajectory.py ->
build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\test_utils.py -> build\lib\AaronTools\test  
copying ..\AaronTools-distro\test\\__init__.py -> build\lib\AaronTools\test  
creating build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\basis.py -> build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\emp_dispersion.py ->
build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\grid.py -> build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\implicit_solvent.py ->
build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\job_types.py ->
build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\method.py -> build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\theory.py -> build\lib\AaronTools\theory  
copying ..\AaronTools-distro\theory\\__init__.py ->
build\lib\AaronTools\theory  
copying ..\AaronTools-distro\bond_data.json -> build\lib\AaronTools  
copying ..\AaronTools-distro\calculated_bond_lengths.json ->
build\lib\AaronTools  
copying ..\AaronTools-distro\config.ini -> build\lib\AaronTools  
copying ..\AaronTools-distro\README.md -> build\lib\AaronTools  
copying ..\AaronTools-distro\LICENSE -> build\lib\AaronTools  
running bdist_wheel  
installing to build\bdist.win-amd64\wheel  
running install  
running install_lib  
creating build\bdist.win-amd64  
creating build\bdist.win-amd64\wheel  
creating build\bdist.win-amd64\wheel\AaronTools  
copying build\lib\AaronTools\atoms.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\bond_data.json -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\calculated_bond_lengths.json -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\component.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\comp_output.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\config.ini -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\config.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\const.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\finders.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\geometry.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\job_control.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\json_extension.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\LICENSE -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\new_fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\README.md -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\ring.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\substituent.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
creating build\bdist.win-amd64\wheel\AaronTools\test  
copying build\lib\AaronTools\test\test_atoms.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_cls.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_component.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_comp_output.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_fetch.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_finders.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_geometry.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_json_extension.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_substituent.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_trajectory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\test_utils.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
copying build\lib\AaronTools\test\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\test  
creating build\bdist.win-amd64\wheel\AaronTools\theory  
copying build\lib\AaronTools\theory\basis.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\emp_dispersion.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\grid.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\implicit_solvent.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\job_types.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\method.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\theory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\theory\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\theory  
copying build\lib\AaronTools\trajectory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
copying build\lib\AaronTools\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools  
creating build\bdist.win-amd64\wheel\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\commands  
copying build\lib\SEQCROW\commands\angle.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\dihedral.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\fuseRing.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\rmsdAlign.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\substitute.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\io.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\jobs.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\libraries.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\managers  
copying build\lib\SEQCROW\managers\filereader_manager.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\job_manager.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\ordered_selection.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\presets.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\residue_collection.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\selectors.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\settings.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\theory.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\tools  
copying build\lib\SEQCROW\tools\aaron_input_builder.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\browse_aarontools.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\compute_thermo.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\filereader_panel.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\input_generator.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\job_manager_tool.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\libadd.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\normal_modes.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\per_frame_plot.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\structure_editing.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\utils.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\comboboxes.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\periodic_table.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
running install_egg_info  
running egg_info  
creating SEQCROW.egg-info  
writing SEQCROW.egg-info\PKG-INFO  
writing dependency_links to SEQCROW.egg-info\dependency_links.txt  
writing requirements to SEQCROW.egg-info\requires.txt  
writing top-level names to SEQCROW.egg-info\top_level.txt  
writing manifest file 'SEQCROW.egg-info\SOURCES.txt'  
reading manifest file 'SEQCROW.egg-info\SOURCES.txt'  
writing manifest file 'SEQCROW.egg-info\SOURCES.txt'  
Copying SEQCROW.egg-info to build\bdist.win-
amd64\wheel\\.\SEQCROW-0.1-py3.7.egg-info  
running install_scripts  
adding license file "license.txt" (matched pattern "LICEN[CS]E*")  
creating build\bdist.win-amd64\wheel\SEQCROW-0.1.dist-info\WHEEL  
creating 'dist\SEQCROW-0.1-py3-none-any.whl' and adding 'build\bdist.win-
amd64\wheel' to it  
adding 'AaronTools/LICENSE'  
adding 'AaronTools/README.md'  
adding 'AaronTools/__init__.py'  
adding 'AaronTools/atoms.py'  
adding 'AaronTools/bond_data.json'  
adding 'AaronTools/calculated_bond_lengths.json'  
adding 'AaronTools/comp_output.py'  
adding 'AaronTools/component.py'  
adding 'AaronTools/config.ini'  
adding 'AaronTools/config.py'  
adding 'AaronTools/const.py'  
adding 'AaronTools/fileIO.py'  
adding 'AaronTools/finders.py'  
adding 'AaronTools/geometry.py'  
adding 'AaronTools/job_control.py'  
adding 'AaronTools/json_extension.py'  
adding 'AaronTools/new_fileIO.py'  
adding 'AaronTools/ring.py'  
adding 'AaronTools/substituent.py'  
adding 'AaronTools/trajectory.py'  
adding 'AaronTools/test/__init__.py'  
adding 'AaronTools/test/test_atoms.py'  
adding 'AaronTools/test/test_cls.py'  
adding 'AaronTools/test/test_comp_output.py'  
adding 'AaronTools/test/test_component.py'  
adding 'AaronTools/test/test_fetch.py'  
adding 'AaronTools/test/test_fileIO.py'  
adding 'AaronTools/test/test_finders.py'  
adding 'AaronTools/test/test_geometry.py'  
adding 'AaronTools/test/test_json_extension.py'  
adding 'AaronTools/test/test_substituent.py'  
adding 'AaronTools/test/test_trajectory.py'  
adding 'AaronTools/test/test_utils.py'  
adding 'AaronTools/theory/__init__.py'  
adding 'AaronTools/theory/basis.py'  
adding 'AaronTools/theory/emp_dispersion.py'  
adding 'AaronTools/theory/grid.py'  
adding 'AaronTools/theory/implicit_solvent.py'  
adding 'AaronTools/theory/job_types.py'  
adding 'AaronTools/theory/method.py'  
adding 'AaronTools/theory/theory.py'  
adding 'SEQCROW/__init__.py'  
adding 'SEQCROW/io.py'  
adding 'SEQCROW/jobs.py'  
adding 'SEQCROW/libraries.py'  
adding 'SEQCROW/presets.py'  
adding 'SEQCROW/residue_collection.py'  
adding 'SEQCROW/selectors.py'  
adding 'SEQCROW/settings.py'  
adding 'SEQCROW/theory.py'  
adding 'SEQCROW/utils.py'  
adding 'SEQCROW/commands/__init__.py'  
adding 'SEQCROW/commands/angle.py'  
adding 'SEQCROW/commands/dihedral.py'  
adding 'SEQCROW/commands/fuseRing.py'  
adding 'SEQCROW/commands/rmsdAlign.py'  
adding 'SEQCROW/commands/substitute.py'  
adding 'SEQCROW/managers/__init__.py'  
adding 'SEQCROW/managers/filereader_manager.py'  
adding 'SEQCROW/managers/job_manager.py'  
adding 'SEQCROW/managers/ordered_selection.py'  
adding 'SEQCROW/tools/__init__.py'  
adding 'SEQCROW/tools/aaron_input_builder.py'  
adding 'SEQCROW/tools/browse_aarontools.py'  
adding 'SEQCROW/tools/compute_thermo.py'  
adding 'SEQCROW/tools/filereader_panel.py'  
adding 'SEQCROW/tools/input_generator.py'  
adding 'SEQCROW/tools/job_manager_tool.py'  
adding 'SEQCROW/tools/libadd.py'  
adding 'SEQCROW/tools/normal_modes.py'  
adding 'SEQCROW/tools/per_frame_plot.py'  
adding 'SEQCROW/tools/structure_editing.py'  
adding 'SEQCROW/widgets/__init__.py'  
adding 'SEQCROW/widgets/comboboxes.py'  
adding 'SEQCROW/widgets/periodic_table.py'  
adding 'SEQCROW-0.1.dist-info/METADATA'  
adding 'SEQCROW-0.1.dist-info/WHEEL'  
adding 'SEQCROW-0.1.dist-info/license.txt'  
adding 'SEQCROW-0.1.dist-info/top_level.txt'  
adding 'SEQCROW-0.1.dist-info/RECORD'  
removing build\bdist.win-amd64\wheel  
Distribution is in C:\Users\Tony
Schaefer\Documents\GitHub\ChimAARON\dist\SEQCROW-0.1-py3-none-any.whl  
  

> devel clean "C:\Users\Tony Schaefer\Documents\GitHub\ChimAARON"

  

> devel build "C:\Users\Tony Schaefer\Documents\GitHub\ChimAARON"

running build  
running build_py  
creating build  
creating build\lib  
creating build\lib\SEQCROW  
copying src\io.py -> build\lib\SEQCROW  
copying src\jobs.py -> build\lib\SEQCROW  
copying src\libraries.py -> build\lib\SEQCROW  
copying src\presets.py -> build\lib\SEQCROW  
copying src\residue_collection.py -> build\lib\SEQCROW  
copying src\selectors.py -> build\lib\SEQCROW  
copying src\settings.py -> build\lib\SEQCROW  
copying src\theory.py -> build\lib\SEQCROW  
copying src\utils.py -> build\lib\SEQCROW  
copying src\\__init__.py -> build\lib\SEQCROW  
creating build\lib\SEQCROW\commands  
copying src\commands\angle.py -> build\lib\SEQCROW\commands  
copying src\commands\dihedral.py -> build\lib\SEQCROW\commands  
copying src\commands\fuseRing.py -> build\lib\SEQCROW\commands  
copying src\commands\rmsdAlign.py -> build\lib\SEQCROW\commands  
copying src\commands\substitute.py -> build\lib\SEQCROW\commands  
copying src\commands\\__init__.py -> build\lib\SEQCROW\commands  
creating build\lib\SEQCROW\managers  
copying src\managers\filereader_manager.py -> build\lib\SEQCROW\managers  
copying src\managers\job_manager.py -> build\lib\SEQCROW\managers  
copying src\managers\ordered_selection.py -> build\lib\SEQCROW\managers  
copying src\managers\\__init__.py -> build\lib\SEQCROW\managers  
creating build\lib\SEQCROW\tools  
copying src\tools\aaron_input_builder.py -> build\lib\SEQCROW\tools  
copying src\tools\browse_aarontools.py -> build\lib\SEQCROW\tools  
copying src\tools\compute_thermo.py -> build\lib\SEQCROW\tools  
copying src\tools\filereader_panel.py -> build\lib\SEQCROW\tools  
copying src\tools\input_generator.py -> build\lib\SEQCROW\tools  
copying src\tools\job_manager_tool.py -> build\lib\SEQCROW\tools  
copying src\tools\libadd.py -> build\lib\SEQCROW\tools  
copying src\tools\normal_modes.py -> build\lib\SEQCROW\tools  
copying src\tools\per_frame_plot.py -> build\lib\SEQCROW\tools  
copying src\tools\structure_editing.py -> build\lib\SEQCROW\tools  
copying src\tools\\__init__.py -> build\lib\SEQCROW\tools  
creating build\lib\SEQCROW\widgets  
copying src\widgets\comboboxes.py -> build\lib\SEQCROW\widgets  
copying src\widgets\periodic_table.py -> build\lib\SEQCROW\widgets  
copying src\widgets\\__init__.py -> build\lib\SEQCROW\widgets  
package init file '..\AaronTools-distro\\__init__.py' not found (or not a
regular file)  
creating build\lib\AaronTools  
creating build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\atoms.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\component.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\comp_output.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\config.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\const.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\fileIO.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\finders.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\geometry.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\job_control.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\json_extension.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\new_fileIO.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\ring.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\substituent.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\trajectory.py -> build\lib\AaronTools\src  
copying ..\AaronTools-distro\src\\__init__.py -> build\lib\AaronTools\src  
creating build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_atoms.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_cls.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_component.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_comp_output.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_fetch.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_fileIO.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_finders.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_geometry.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_json_extension.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_substituent.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_trajectory.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\test_utils.py ->
build\lib\AaronTools\src\test  
copying ..\AaronTools-distro\src\test\\__init__.py ->
build\lib\AaronTools\src\test  
creating build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\basis.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\emp_dispersion.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\grid.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\implicit_solvent.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\job_types.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\method.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\theory.py ->
build\lib\AaronTools\src\theory  
copying ..\AaronTools-distro\src\theory\\__init__.py ->
build\lib\AaronTools\src\theory  
running bdist_wheel  
installing to build\bdist.win-amd64\wheel  
running install  
running install_lib  
creating build\bdist.win-amd64  
creating build\bdist.win-amd64\wheel  
creating build\bdist.win-amd64\wheel\AaronTools  
creating build\bdist.win-amd64\wheel\AaronTools\src  
copying build\lib\AaronTools\src\atoms.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\component.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\comp_output.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\config.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\const.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\finders.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\geometry.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\job_control.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\json_extension.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\new_fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\ring.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\substituent.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
creating build\bdist.win-amd64\wheel\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_atoms.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_cls.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_component.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_comp_output.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_fetch.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_fileIO.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_finders.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_geometry.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_json_extension.py ->
build\bdist.win-amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_substituent.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_trajectory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\test_utils.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
copying build\lib\AaronTools\src\test\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\test  
creating build\bdist.win-amd64\wheel\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\basis.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\emp_dispersion.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\grid.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\implicit_solvent.py ->
build\bdist.win-amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\job_types.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\method.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\theory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\theory\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src\theory  
copying build\lib\AaronTools\src\trajectory.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
copying build\lib\AaronTools\src\\__init__.py -> build\bdist.win-
amd64\wheel\\.\AaronTools\src  
creating build\bdist.win-amd64\wheel\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\commands  
copying build\lib\SEQCROW\commands\angle.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\dihedral.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\fuseRing.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\rmsdAlign.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\substitute.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\commands\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\commands  
copying build\lib\SEQCROW\io.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\jobs.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\libraries.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\managers  
copying build\lib\SEQCROW\managers\filereader_manager.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\job_manager.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\ordered_selection.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\managers\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\managers  
copying build\lib\SEQCROW\presets.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\residue_collection.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\selectors.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\settings.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
copying build\lib\SEQCROW\theory.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\tools  
copying build\lib\SEQCROW\tools\aaron_input_builder.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\browse_aarontools.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\compute_thermo.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\filereader_panel.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\input_generator.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\job_manager_tool.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\libadd.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\normal_modes.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\per_frame_plot.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\structure_editing.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\tools\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\tools  
copying build\lib\SEQCROW\utils.py -> build\bdist.win-amd64\wheel\\.\SEQCROW  
creating build\bdist.win-amd64\wheel\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\comboboxes.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\periodic_table.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\widgets\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW\widgets  
copying build\lib\SEQCROW\\__init__.py -> build\bdist.win-
amd64\wheel\\.\SEQCROW  
running install_egg_info  
running egg_info  
creating SEQCROW.egg-info  
writing SEQCROW.egg-info\PKG-INFO  
writing dependency_links to SEQCROW.egg-info\dependency_links.txt  
writing requirements to SEQCROW.egg-info\requires.txt  
writing top-level names to SEQCROW.egg-info\top_level.txt  
writing manifest file 'SEQCROW.egg-info\SOURCES.txt'  
reading manifest file 'SEQCROW.egg-info\SOURCES.txt'  
writing manifest file 'SEQCROW.egg-info\SOURCES.txt'  
Copying SEQCROW.egg-info to build\bdist.win-
amd64\wheel\\.\SEQCROW-0.1-py3.7.egg-info  
running install_scripts  
adding license file "license.txt" (matched pattern "LICEN[CS]E*")  
creating build\bdist.win-amd64\wheel\SEQCROW-0.1.dist-info\WHEEL  
creating 'dist\SEQCROW-0.1-py3-none-any.whl' and adding 'build\bdist.win-
amd64\wheel' to it  
adding 'AaronTools/src/__init__.py'  
adding 'AaronTools/src/atoms.py'  
adding 'AaronTools/src/comp_output.py'  
adding 'AaronTools/src/component.py'  
adding 'AaronTools/src/config.py'  
adding 'AaronTools/src/const.py'  
adding 'AaronTools/src/fileIO.py'  
adding 'AaronTools/src/finders.py'  
adding 'AaronTools/src/geometry.py'  
adding 'AaronTools/src/job_control.py'  
adding 'AaronTools/src/json_extension.py'  
adding 'AaronTools/src/new_fileIO.py'  
adding 'AaronTools/src/ring.py'  
adding 'AaronTools/src/substituent.py'  
adding 'AaronTools/src/trajectory.py'  
adding 'AaronTools/src/test/__init__.py'  
adding 'AaronTools/src/test/test_atoms.py'  
adding 'AaronTools/src/test/test_cls.py'  
adding 'AaronTools/src/test/test_comp_output.py'  
adding 'AaronTools/src/test/test_component.py'  
adding 'AaronTools/src/test/test_fetch.py'  
adding 'AaronTools/src/test/test_fileIO.py'  
adding 'AaronTools/src/test/test_finders.py'  
adding 'AaronTools/src/test/test_geometry.py'  
adding 'AaronTools/src/test/test_json_extension.py'  
adding 'AaronTools/src/test/test_substituent.py'  
adding 'AaronTools/src/test/test_trajectory.py'  
adding 'AaronTools/src/test/test_utils.py'  
adding 'AaronTools/src/theory/__init__.py'  
adding 'AaronTools/src/theory/basis.py'  
adding 'AaronTools/src/theory/emp_dispersion.py'  
adding 'AaronTools/src/theory/grid.py'  
adding 'AaronTools/src/theory/implicit_solvent.py'  
adding 'AaronTools/src/theory/job_types.py'  
adding 'AaronTools/src/theory/method.py'  
adding 'AaronTools/src/theory/theory.py'  
adding 'SEQCROW/__init__.py'  
adding 'SEQCROW/io.py'  
adding 'SEQCROW/jobs.py'  
adding 'SEQCROW/libraries.py'  
adding 'SEQCROW/presets.py'  
adding 'SEQCROW/residue_collection.py'  
adding 'SEQCROW/selectors.py'  
adding 'SEQCROW/settings.py'  
adding 'SEQCROW/theory.py'  
adding 'SEQCROW/utils.py'  
adding 'SEQCROW/commands/__init__.py'  
adding 'SEQCROW/commands/angle.py'  
adding 'SEQCROW/commands/dihedral.py'  
adding 'SEQCROW/commands/fuseRing.py'  
adding 'SEQCROW/commands/rmsdAlign.py'  
adding 'SEQCROW/commands/substitute.py'  
adding 'SEQCROW/managers/__init__.py'  
adding 'SEQCROW/managers/filereader_manager.py'  
adding 'SEQCROW/managers/job_manager.py'  
adding 'SEQCROW/managers/ordered_selection.py'  
adding 'SEQCROW/tools/__init__.py'  
adding 'SEQCROW/tools/aaron_input_builder.py'  
adding 'SEQCROW/tools/browse_aarontools.py'  
adding 'SEQCROW/tools/compute_thermo.py'  
adding 'SEQCROW/tools/filereader_panel.py'  
adding 'SEQCROW/tools/input_generator.py'  
adding 'SEQCROW/tools/job_manager_tool.py'  
adding 'SEQCROW/tools/libadd.py'  
adding 'SEQCROW/tools/normal_modes.py'  
adding 'SEQCROW/tools/per_frame_plot.py'  
adding 'SEQCROW/tools/structure_editing.py'  
adding 'SEQCROW/widgets/__init__.py'  
adding 'SEQCROW/widgets/comboboxes.py'  
adding 'SEQCROW/widgets/periodic_table.py'  
adding 'SEQCROW-0.1.dist-info/METADATA'  
adding 'SEQCROW-0.1.dist-info/WHEEL'  
adding 'SEQCROW-0.1.dist-info/license.txt'  
adding 'SEQCROW-0.1.dist-info/top_level.txt'  
adding 'SEQCROW-0.1.dist-info/RECORD'  
removing build\bdist.win-amd64\wheel  
Distribution is in C:\Users\Tony
Schaefer\Documents\GitHub\ChimAARON\dist\SEQCROW-0.1-py3-none-any.whl  
  




OpenGL version: 3.3.0 NVIDIA 456.38
OpenGL renderer: GeForce RTX 2070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Education (Build 17763)
Memory: 17,107,533,824
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 2700X Eight-Core Processor         "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
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    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
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    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
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    ChimeraX-CellPack: 1.0
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    ChimeraX-ChemGroup: 2.0
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    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
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    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
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    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
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    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
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    ChimeraX-MapFit: 2.0
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    ChimeraX-MedicalToolbar: 1.0.1
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    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (7)

comment:1 by pett, 5 years ago

Cc:	chimera-programmers Tristan Croll added
Component:	Unassigned → Build System
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Bundle builder: DataDir from extra package not copied

comment:2 by Tristan Croll, 5 years ago

I'm not familiar with the AdditionalPackages tag. Is that new?

comment:3 by pett, 5 years ago

Tony, it looks like a bug in Bundle Builder where it's using a hard-coded "src" instead of your "folder" attribute. I'll try to fix that today.

Tristan, the AdditionalPackages tag was added more than 3 years ago.

in reply to: 4 ; follow-up: 4 comment:4 by Tristan Croll, 5 years ago

Huh. How time flies...
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 23 September 2020 19:42
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>; tony.schaefer@uga.edu <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #3750: Bundle builder: DataDir from extra package not copied

#3750: Bundle builder: DataDir from extra package not copied
--------------------------------------+------------------------
          Reporter:  tony.schaefer@…  |      Owner:  Greg Couch
              Type:  defect           |     Status:  assigned
          Priority:  normal           |  Milestone:
         Component:  Build System     |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+------------------------

Comment (by Eric Pettersen):

 Tony, it looks like a bug in Bundle Builder where it's using a hard-coded
 "src" instead of your "folder" attribute.  I'll try to fix that today.

 Tristan, the !AdditionalPackages tag was added more than 3 years ago.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3750#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by pett, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Hi Tony,

I have committed a fix. None of the bundles we have use the AdditionalPackages tag, so I had to jury rig something to test the change. It did something which I think is correct, but you will have to confirm.
The "fix" will be in tomorrow's builds. We have been having issues with the builds lately due to other changes, but there's is some chance they will work -- particularly on Mac, which I can test directly on here at home.

--Eric

in reply to: 6 ; follow-up: 6 comment:6 by tony.schaefer@…, 5 years ago

Eric,

The fix works for me!

Thanks,

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, September 23, 2020 6:18 PM
Cc: chimera-programmers@cgl.ucsf.edu <chimera-programmers@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #3750: Bundle builder: DataDir from extra package not copied

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#3750: Bundle builder: DataDir from extra package not copied
--------------------------------------+------------------------
          Reporter:  tony.schaefer@…  |      Owner:  Greg Couch
              Type:  defect           |     Status:  closed
          Priority:  normal           |  Milestone:
         Component:  Build System     |    Version:
        Resolution:  fixed            |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+------------------------
Changes (by Eric Pettersen):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Hi Tony,
         I have committed a fix.  None of the bundles we have use the
 `AdditionalPackages` tag, so I had to jury rig something to test the
 change.  It did **something** which I **think** is correct, but you will
 have to confirm.
         The "fix" will be in tomorrow's builds.  We have been having
 issues with the builds lately due to other changes, but there's is some
 chance they will work -- particularly on Mac, which I can test directly on
 here at home.

 --Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3750#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:7 by pett, 5 years ago

Great!

--Eric

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