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Complete the exts_list to avoid missing deps issues #12

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a710a8b
Add .venv* to .gitignore file
Oct 28, 2024
f47e912
Update exts_list versions implemented
Oct 28, 2024
51d521f
Minior fixes to match EB style
dagonzalezfo Oct 30, 2024
8e77236
Delete printing magic numbers offsets
Oct 31, 2024
4653be7
Change NotImplementedError for EasyBuildError
Oct 31, 2024
fa11840
Avoid direct references to class variables from outside the class.
Oct 31, 2024
fab8112
Improved variable string type check when writing down options in new …
Oct 31, 2024
7bbf2e4
Added support for bioconductor packages
Oct 31, 2024
df2b442
clean code
Nov 4, 2024
7eaa222
Merge pull request #7 from HPCNow/feature-update-exts-list-versions-t…
macheitor Nov 7, 2024
3374b22
Update_exts_list outside of EasyBlock class
Nov 8, 2024
dbe9d65
Refactor magic string
Nov 8, 2024
0e30a6e
Getters for exts_list, exts_defaultclass and bioconductor_version.
Nov 11, 2024
b172db8
Implemented crosscheck between exts_list and extensions installed by …
Nov 12, 2024
c5703c1
Avoid getting the exts_list of the orginal easyconfig
Nov 14, 2024
bf56361
Do not update extensions that are on base R
Nov 14, 2024
7d01f4c
Fix update exts list with base R extensions
Nov 14, 2024
e9a60f9
Fix R base packages
Nov 14, 2024
aaacf9d
CleanCode
Nov 15, 2024
1f9a1aa
Clarify case where extensions in exts_list is a string
Nov 15, 2024
663211a
Calculate MD5 checksum for R packages that do not have MD5 in their C…
Nov 15, 2024
9146cd2
Merge branch 'develop' into feature-update-exts-list-versions-to-latest
Nov 15, 2024
22de1aa
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 15, 2024
ee73df9
Clean code and minor comments
Nov 15, 2024
2295983
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 15, 2024
7e3d7c5
Unify destructuring extensions
Nov 15, 2024
40bf8d2
Clean code and improvement of error handling
Nov 20, 2024
4b0ae39
Clean code and minor improvements
Nov 20, 2024
5622557
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 20, 2024
b916a38
Clean code and minor improvements
Nov 20, 2024
6888b8b
Delete get_exts_list console messages
Nov 20, 2024
23efa0d
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 20, 2024
886716d
spelling error
Nov 21, 2024
2be731e
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 21, 2024
272c779
Added pythonBundle easyblock check for deducing exts_defaultclass in …
Nov 21, 2024
6500758
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 21, 2024
5e34872
Fix recursivity issue: we were not storing extensions of bottom of re…
Nov 21, 2024
5039cf4
Clean code and error check
Nov 21, 2024
f4fb003
Add .vscode folder to the .gitignore file
Nov 22, 2024
5eca48d
Gather update exts feature into exts_tools.py file
Nov 22, 2024
b0d6ef2
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 22, 2024
83eb6fc
Add _get_extension_values function
Nov 22, 2024
f0bf88b
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 22, 2024
09a74ae
Delete trail space
Nov 22, 2024
f4d7fc4
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 22, 2024
2182bd9
Get rid of _calculate_md5 function
Nov 22, 2024
0261601
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Nov 22, 2024
5563d45
Delete .vscode files from git repo
Nov 22, 2024
a20fb5c
Delete unwanted easyblock changes
Nov 22, 2024
d50b376
Unifying PRs
Nov 22, 2024
6bee79c
Clean code and clean output in terminal
Nov 25, 2024
60d8ecf
--complete-exts-list for R implemented
Nov 26, 2024
c781bd8
Improve output messaging
Nov 26, 2024
cde7450
Merge branch 'feature-repeated-exts-list' into feature-complete-exts-…
Nov 26, 2024
a7b7247
Improved messaging
Nov 26, 2024
b62d621
Clean code and improve terminal messaging
Nov 27, 2024
5343de9
Minor terminal output improvements
Nov 27, 2024
1da7dba
terminal output improvements
Nov 27, 2024
2e1120a
bugfix
Nov 27, 2024
89c9d19
terminal output improve
Nov 27, 2024
d8386dc
Remove duplicates from exts_list
Nov 28, 2024
5f4008b
Bugfix recursive call for R dependencies
Nov 29, 2024
9f6dcba
Unify extensions check flag name
Nov 29, 2024
7ab493f
Merge branch 'feature-repeated-exts-list' into feature-complete-exts-…
Nov 29, 2024
b7dc7ea
Separation of concerns on complete_R_exts_list functions
Nov 29, 2024
ac8950e
Minor terminal output improvement
Nov 29, 2024
f51251f
Bugfix when merging check_exts_list with complete_exts_list
Nov 29, 2024
9b618cd
Bugfix check_exts_list call
Nov 29, 2024
c915800
Merge branch 'feature-repeated-exts-list' into feature-complete-exts-…
Nov 29, 2024
3e7217e
complete-exts-list is implementation improved by using a dependency g…
macheitor Nov 30, 2024
9c6299a
terminal output improvement
macheitor Nov 30, 2024
b07ea12
edges in dependency graph are a single value not array
macheitor Nov 30, 2024
bd0c3ae
Bugfix: missing dependencies if dep already processed fixed
macheitor Nov 30, 2024
23363b3
Revert "edges in dependency graph are a single value not array"
macheitor Nov 30, 2024
6dead14
Revert "Revert "edges in dependency graph are a single value not array""
macheitor Nov 30, 2024
858a4f9
Revert "Bugfix: missing dependencies if dep already processed fixed"
macheitor Nov 30, 2024
4a721ee
Revert "edges in dependency graph are a single value not array"
macheitor Nov 30, 2024
1cb61ff
Using graphs for complete_exts_list
macheitor Nov 30, 2024
71b88be
get installed exts is processed using parallel threads
Dec 2, 2024
8ea6776
Improve terminal output in while getting extensions
macheitor Dec 2, 2024
4eff58d
fulfill extensions is now parallel
Dec 3, 2024
77569b1
Update extensions is now parallel
Dec 3, 2024
6934a82
Merge branch 'feature-update-exts-list-versions-to-latest' into featu…
Dec 3, 2024
dd9e2ab
Merge branch 'feature-repeated-exts-list' into feature-complete-exts-…
Dec 3, 2024
5489338
removing duplicated function
Dec 3, 2024
742b5a7
Get R dependencies processed in parallel
Dec 3, 2024
4b3d03f
Added TODO comment
Dec 4, 2024
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@ dist/
*egg-info/
*.swp
.mypy_cache/

.venv*
.vscode/
Dockerfile.*
Singularity.*
test-reports/
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