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Enhance availability of refineGEMs #85

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2 tasks
GwennyGit opened this issue May 4, 2023 · 4 comments
Open
2 tasks

Enhance availability of refineGEMs #85

GwennyGit opened this issue May 4, 2023 · 4 comments
Labels
enhancement New feature or request
Milestone
New functions tow...

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@GwennyGit
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GwennyGit commented May 4, 2023 •
edited
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To enhance the availability of the whole refineGEMs package I would suggest the following options:
@GwennyGit GwennyGit added the enhancement New feature or request label May 4, 2023
famosab added a commit that referenced this issue May 9, 2023
@famosab
Enable docs #85
524782b
famosab added a commit that referenced this issue May 9, 2023
@famosab
Add nbsphinx #85
abc20eb
famosab added a commit that referenced this issue May 9, 2023
@famosab
Add nbsphinx #85
0fee61d
GwennyGit added a commit that referenced this issue Jul 6, 2023
@GwennyGit
Created workflow to publish new release from GitHub in PyPi #85
2d9a14b
GwennyGit added a commit that referenced this issue Jul 6, 2023
@GwennyGit
Adjusted version in pipfile.lock #85
fc2e507
GwennyGit added a commit that referenced this issue Jul 10, 2023
@GwennyGit
Updated DOI badge in README #85
73a462a
GwennyGit added a commit that referenced this issue Jul 13, 2023
@GwennyGit
Changed the workflow for PyPi publication #85
f5930b6 
Needed to change the workflow to only be triggered via workflow_dispatch as the pushing to test-pypi did not work and as it is safer to trigger it manually then automatically.
GwennyGit added a commit that referenced this issue Jul 13, 2023
@GwennyGit
Removed old workflow to publish to test PyPi and PyPi #85
2165047 
Needed to remove the old version as the changed file was renamed
GwennyGit added a commit that referenced this issue Aug 18, 2023
@GwennyGit
Moved database folder from data into package refinegems #49 #85
19cf067 
To make functions accessing the database functional within user scripts I had to move the files into the package folder.
GwennyGit added a commit that referenced this issue Aug 18, 2023
@GwennyGit
Changed setup.py to include the database files in the installation #49 …
26ab5b3 
…#85
GwennyGit added a commit that referenced this issue Aug 18, 2023
@GwennyGit
Try another approach to include database in installation #49 #85
4b0ce7e
@GwennyGit
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For task 1, another idea would be to split the tool into different entry points. One for model investigation, one for model refinement and one for model curation.

How to achieve?

  • Generate four 'main' modules/ command line names: data, investigate, refine and curate
  • Extract code from io and main for the relevant modules per new 'main' module (see table)
  • Add entry points to the setup.py
'Main' module/Command line name Relevant modules Description
data databases Handles database input/output & initialisation
investigate comparison, growth, investigate, gapfill.gap_analysis Handles model comparison, growth simulation & other types of model investigation
refine biomass, charges, modelseed, pathways, polish, sboann Handles all possible refinement techniques implemented in refineGEMs
curate curate, gapfill.gapfill_model Handles the curation implementations of refineGEMs

GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Added python_requires into setup.py #85
dfad0ee
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Created setup.cfg with possible entry point setup #85
c5dae3a
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GwennyGit commented Aug 21, 2023 •
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The setup.py should be replaced by a setup.cfg as the setup.py file is legacy and might get deprecated. A possible setup.cfg, already including the setup for the possible entry points, was generated and uploaded to the branch structure_update.

As with refineGEMs 1.4.0 the pyproject.toml file was adjusted so that the complete install is only handled by the pyproject.toml. This deprecates the setup.cfg which is now removed with the commit Removed no longer needed setup.cfg. The already existing entry points were moved as comments to the pyproject.toml file with the commit Added entry points as comments to pyproject.toml and need to be tested and adjusted before use.

GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Moved database folder from data into package refinegems #49 #85
c9dfa9d 
To make functions accessing the database functional within user scripts I had to move the files into the package folder.
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Moved database folder from data into package refinegems #49 #85
665b034 
To make functions accessing the database functional within user scripts I had to move the files into the package folder.
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Changed setup.py to include the database files in the installation #49 …
aaa9ad3 
…#85
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Try another approach to include database in installation #49 #85
20bdf38
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Added python_requires into setup.py #85
d9517f0
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Moved database folder from data into package refinegems #49 #85
65c3893 
To make functions accessing the database functional within user scripts I had to move the files into the package folder.
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Changed setup.py to include the database files in the installation #49 …
2c8821e 
…#85
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Try another approach to include database in installation #49 #85
e28216d
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Added python_requires into setup.py #85
fc8ec91
@GwennyGit
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All commits from the last comment to this comment are the result of my attempt to rebase these commits from dev to another branch. However, this did not work and, thus, I will cherry-pick the according commits to the other branch. This will likely add the same commits again in this issue after this comment.

GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Moved database folder from data into package refinegems #49 #85
b1eaa22 
To make functions accessing the database functional within user scripts I had to move the files into the package folder.
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Changed setup.py to include the database files in the installation #49 …
a26926d 
…#85
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Try another approach to include database in installation #49 #85
048135b
GwennyGit added a commit that referenced this issue Aug 21, 2023
@GwennyGit
Added python_requires into setup.py #85
1f3be81
GwennyGit added a commit that referenced this issue Sep 18, 2023
@GwennyGit
Removed broken Pipfile & Pipfile.lock #85
6e3edc2 
I broke the setup of Pipfile & Pipfile.lock and I found no solution to fix or update both files. Moreover, I think these files are obsolete and unneccesary to be distributed. Thus, I removed the files from the package completely.
GwennyGit added a commit that referenced this issue Sep 22, 2023
@GwennyGit
Added Python version requirement to additionally to TOML file #85
d7a3765
f3rryman added a commit that referenced this issue Sep 27, 2023
@f3rryman
Bug fixes for dependencies #85
cf8b6e7 
minor bug fixes
GwennyGit added a commit that referenced this issue Oct 4, 2023
@GwennyGit
Added version number in pyproject.toml #85
875d908
GwennyGit added a commit that referenced this issue Oct 30, 2023
@GwennyGit
Added depinfo restrictions to setup.py #85
74bbbfb
GwennyGit added a commit that referenced this issue Nov 13, 2023
@GwennyGit
Added depinfo restrictions to setup.py #85
c464bb1
GwennyGit added a commit that referenced this issue Nov 13, 2023
@GwennyGit
Created setup.cfg with possible entry point setup #85
3229b53
GwennyGit added a commit that referenced this issue Nov 14, 2023
@GwennyGit
Removed unnecessary zip_safe #85
9d71930
GwennyGit added a commit that referenced this issue Nov 14, 2023
@GwennyGit
Added entry points as comments to pyproject.toml #85
ef8b480
GwennyGit added a commit that referenced this issue Nov 14, 2023
@GwennyGit
Removed no longer needed setup.cfg #85
a460e4a
GwennyGit added a commit that referenced this issue Jan 10, 2024
@GwennyGit
Restructured refineGEMs folder structure #85
01a1a8c
@cb-Hades
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cb-Hades commented Jan 10, 2024 •
edited
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Currently, refineGEMs works for python 3.10 and 3.9.
Release 2.0.0 should work under 3.10 and 3.11

  • 3.10
  • 3.11
  • 3.12
  • 3.13

cb-Hades added a commit that referenced this issue Feb 8, 2024
@cb-Hades
developement update
18e6229 
- added ideas and possible new code for io #85, #44 and investigate to CB_under_construction
- bit of restructering in io and investigate
- bit of Specimen integration in new code block CB_under_construction #99
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