Enhance availability of refineGEMs #85

GwennyGit · 2023-05-04T13:14:16Z

To enhance the availability of the whole refineGEMs package I would suggest the following options:

Task 1: Evaluate & add entry points #118
Task 2: Provide refineGEMs also via conda

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.

Needed to remove the old version as the changed file was renamed

To make functions accessing the database functional within user scripts I had to move the files into the package folder.

…#85

GwennyGit · 2023-08-21T10:50:28Z

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 · 2023-08-21T11:05:04Z

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.

To make functions accessing the database functional within user scripts I had to move the files into the package folder.

…#85

To make functions accessing the database functional within user scripts I had to move the files into the package folder.

…#85

GwennyGit · 2023-08-21T13:46:47Z

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.

To make functions accessing the database functional within user scripts I had to move the files into the package folder.

…#85

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.

minor bug fixes

cb-Hades · 2024-01-10T14:24:05Z

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

- 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

GwennyGit added the enhancement New feature or request label May 4, 2023

GwennyGit added this to the New functions towards a version 1.1 milestone May 4, 2023

famosab added a commit that referenced this issue May 9, 2023

Enable docs #85

524782b

famosab added a commit that referenced this issue May 9, 2023

Add nbsphinx #85

abc20eb

famosab added a commit that referenced this issue May 9, 2023

Add nbsphinx #85

0fee61d

GwennyGit added a commit that referenced this issue Jul 6, 2023

Created workflow to publish new release from GitHub in PyPi #85

2d9a14b

GwennyGit added a commit that referenced this issue Jul 6, 2023

Adjusted version in pipfile.lock #85

fc2e507

GwennyGit added a commit that referenced this issue Jul 10, 2023

Updated DOI badge in README #85

73a462a

GwennyGit added a commit that referenced this issue Jul 13, 2023

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

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

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

Try another approach to include database in installation #49 #85

4b0ce7e

GwennyGit added a commit that referenced this issue Aug 21, 2023

Added python_requires into setup.py #85

dfad0ee

GwennyGit added a commit that referenced this issue Aug 21, 2023

Created setup.cfg with possible entry point setup #85

c5dae3a

GwennyGit added a commit that referenced this issue Aug 21, 2023

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

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

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

Try another approach to include database in installation #49 #85

20bdf38

GwennyGit added a commit that referenced this issue Aug 21, 2023

Added python_requires into setup.py #85

d9517f0

GwennyGit added a commit that referenced this issue Aug 21, 2023

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

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

Try another approach to include database in installation #49 #85

e28216d

GwennyGit added a commit that referenced this issue Aug 21, 2023

Added python_requires into setup.py #85

fc8ec91

GwennyGit added a commit that referenced this issue Aug 21, 2023

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

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

Try another approach to include database in installation #49 #85

048135b

GwennyGit added a commit that referenced this issue Aug 21, 2023

Added python_requires into setup.py #85

1f3be81

GwennyGit added a commit that referenced this issue Sep 22, 2023

Added Python version requirement to additionally to TOML file #85

d7a3765

f3rryman added a commit that referenced this issue Sep 27, 2023

Bug fixes for dependencies #85

cf8b6e7

minor bug fixes

GwennyGit added a commit that referenced this issue Oct 4, 2023

Added version number in pyproject.toml #85

875d908

GwennyGit added a commit that referenced this issue Oct 30, 2023

Added depinfo restrictions to setup.py #85

74bbbfb

GwennyGit added a commit that referenced this issue Nov 13, 2023

Added depinfo restrictions to setup.py #85

c464bb1

GwennyGit added a commit that referenced this issue Nov 13, 2023

Created setup.cfg with possible entry point setup #85

3229b53

GwennyGit added a commit that referenced this issue Nov 14, 2023

Removed unnecessary zip_safe #85

9d71930

GwennyGit added a commit that referenced this issue Nov 14, 2023

Added entry points as comments to pyproject.toml #85

ef8b480

GwennyGit added a commit that referenced this issue Nov 14, 2023

Removed no longer needed setup.cfg #85

a460e4a

GwennyGit added a commit that referenced this issue Jan 10, 2024

Restructured refineGEMs folder structure #85

01a1a8c

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Enhance availability of refineGEMs #85

Enhance availability of refineGEMs #85

GwennyGit commented May 4, 2023 •

edited

GwennyGit commented Aug 21, 2023

GwennyGit commented Aug 21, 2023 •

edited

GwennyGit commented Aug 21, 2023

cb-Hades commented Jan 10, 2024

Enhance availability of refineGEMs #85

Enhance availability of refineGEMs #85

Comments

GwennyGit commented May 4, 2023 • edited

GwennyGit commented Aug 21, 2023

GwennyGit commented Aug 21, 2023 • edited

GwennyGit commented Aug 21, 2023

cb-Hades commented Jan 10, 2024

GwennyGit commented May 4, 2023 •

edited

GwennyGit commented Aug 21, 2023 •

edited