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feat: memote #239

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Apr 23, 2021
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6034d8d
feat-data: add new GPRs for transport rxns
feiranl Nov 16, 2018
7cc057f
feat-rxn.annota: update new GPRs for those transport rxns
feiranl Nov 16, 2018
31a4ce4
feat-data: add tranport gene annotation from TCDB database
Nov 19, 2018
323975e
Merge branch 'devel' into AddTransGPR
BenjaSanchez Nov 30, 2018
1757426
doc: citation guidelines
BenjaSanchez Nov 30, 2018
51b259c
feat: Zenodo badge
BenjaSanchez Nov 30, 2018
21a2b4b
feat-function: update the function
feiranl Nov 30, 2018
64927c3
feat-rxn.annot: update confidence scores for those transport rxns
feiranl Nov 30, 2018
39bfdc2
Merge pull request #181 from SysBioChalmers/doc/citationGuidelines
BenjaSanchez Dec 4, 2018
34a34fc
doc: added contributors
BenjaSanchez Dec 4, 2018
f88f507
style-data:add a title to the file 'biomassComposition_Cofactor_Ion.tsv'
feiranl Dec 4, 2018
1715d0a
fix-data: update the data with Ca2+ exchange reaction
feiranl Dec 4, 2018
c6dc07b
feat-rxns: add Ca2+ exchange reaction
feiranl Dec 4, 2018
c1ecddc
fix-rxnannot:fix the rxnconfidence scores for those reactions in this…
feiranl Dec 5, 2018
8aef65c
Merge pull request #183 from SysBioChalmers/fix-biomass
BenjaSanchez Dec 6, 2018
cb67932
chore: update dependencies
BenjaSanchez Dec 6, 2018
d902f73
Merge branch 'devel' into AddTransGPR
BenjaSanchez Dec 6, 2018
da7dcec
Merge pull request #178 from SysBioChalmers/AddTransGPR
BenjaSanchez Dec 6, 2018
9451f05
fix-data: empty rows
BenjaSanchez Dec 6, 2018
5c4f58d
fix-data: carbohydrate formulas
BenjaSanchez Dec 6, 2018
763a9fd
feat-met.prop: chemical formulas
BenjaSanchez Dec 6, 2018
e0b6846
Merge pull request #155 from wtscott31/fix/metFormulas
BenjaSanchez Dec 11, 2018
1e33c64
feat-func: add a function to deteact deadends that can be solved by a…
feiranl Feb 6, 2019
cb111e6
feat-data: add gapfilling rxns and function to update the model
feiranl Feb 6, 2019
4e7af57
feat-rxn: add gapfilling rxns into the model
feiranl Feb 6, 2019
37a5569
fix-correct a gene name for one rxn
feiranl Feb 6, 2019
3b83df2
feat-met.BiGGID: add BiGG identifiers for metabolites and reactions
snmendoz Mar 15, 2019
a1a5b2f
fix/FAEsters_Addition
wtscott31 Apr 11, 2019
43dd80e
Merge pull request #186 from SysBioChalmers/correct-gene-rule
BenjaSanchez May 3, 2019
90a984f
Merge branch 'devel' into gapfilling
BenjaSanchez May 13, 2019
982a68d
style: proper indentation to scripts
BenjaSanchez May 13, 2019
789533d
feat: update the rxnnotes for gapfilling rxns
feiranl May 20, 2019
8018098
feat: add more annotation in the function
feiranl May 20, 2019
3bff1d8
feat-func: optimize the function
feiranl May 21, 2019
a3cd4e8
chore-rxnannota: add a prefix for rxnAnnotation of Bigg ID
feiranl May 22, 2019
3f9dcf0
Merge pull request #185 from SysBioChalmers/gapfilling
BenjaSanchez May 23, 2019
e1a9644
doc-func: change some varibales in function MissingTransDeadEnd to cl…
feiranl Jul 22, 2019
eb07620
Merge pull request #195 from SysBioChalmers/fix_gapfilling_confusion
BenjaSanchez Jul 26, 2019
d6949e4
chore: update dependencies
BenjaSanchez Jul 28, 2019
5c52afb
fix-data: remove unexpected characters
BenjaSanchez Aug 28, 2019
346edc0
feat-function: update the function to fix anaerobic growth
feiranl Sep 24, 2019
fde588f
feat-function: add a function to rescale the nitrogen limited conditi…
feiranl Sep 24, 2019
269fbbd
feat-Growth function for figS4c for yeast8 paper
feiranl Sep 24, 2019
7bcf7a5
feat-add a function to test essential genes
feiranl Sep 24, 2019
511aadc
feat-update several functions to delete redundant lines.
feiranl Oct 2, 2019
eb2e695
feat-update the function notes
feiranl Oct 2, 2019
1a53af9
feat-change the location for meanerror in the figure
feiranl Oct 2, 2019
529901f
style: folder naming
Nov 5, 2019
4714646
fix: cd to right places
Nov 5, 2019
13d3fd1
style: misc changes in format
Nov 5, 2019
b8ec446
fix: revert scaleBioMass to original version
Nov 5, 2019
aa2564d
refactor: scaleBioMass
Nov 5, 2019
c6a767d
feat: generalize sumBioMass to not require data
Nov 5, 2019
fbf88a2
refactor: scaleBioMass function
Nov 5, 2019
9f91753
fix: lipid rescaling
Nov 5, 2019
3d165e6
Merge pull request #199 from SysBioChalmers/feat-anaerobicgrowth
BenjaSanchez Nov 11, 2019
8a98cd4
refactor: rename folder/file
BenjaSanchez Dec 26, 2019
72b7219
style: essentialGenes
BenjaSanchez Jan 1, 2020
d86554e
chore: move manual curation scripts
BenjaSanchez Mar 20, 2020
2db7146
chore: move other scripts
BenjaSanchez Mar 20, 2020
1ce22e0
doc: add readme files to script/data folders
BenjaSanchez Mar 20, 2020
5054f75
fix: shorten readme file
BenjaSanchez Mar 20, 2020
327ff2d
refactor: remove redundant changes in essentialGenes
BenjaSanchez Mar 24, 2020
aedb78e
Merge pull request #200 from SysBioChalmers/feat-essentialGenes
BenjaSanchez Mar 24, 2020
d0b4e0b
Merge pull request #209 from SysBioChalmers/chore/move-deprecated-scr…
edkerk Mar 24, 2020
2e5460c
doc: simplify templates
BenjaSanchez Mar 27, 2020
ac52a14
doc: update citation guidelines
BenjaSanchez Mar 27, 2020
93f2594
doc: update contribution guidelines
BenjaSanchez Mar 27, 2020
0d6aa78
fix: tabs in contributing guidelines
BenjaSanchez Mar 27, 2020
215bce4
Merge pull request #210 from SysBioChalmers/doc/update-guidelines
BenjaSanchez Mar 30, 2020
ff677f1
fix: remove non-s288c genes
BenjaSanchez Mar 31, 2020
f2f41c1
Merge pull request #211 from SysBioChalmers/fix/removeWrongGenes
BenjaSanchez Apr 1, 2020
52c24ab
test: model properly loaded by cobrapy
BenjaSanchez Apr 21, 2020
434d240
fix: replace proteins with geneNames
BenjaSanchez Apr 21, 2020
4722c45
Merge pull request #216 from SysBioChalmers/fix/gene-names
BenjaSanchez Apr 24, 2020
325be62
Revert "feat-met.BiGGID: add BiGG identifiers for metabolites and rea…
BenjaSanchez Apr 24, 2020
0a8150a
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez Apr 27, 2020
ff435cb
fix-met.annot: KEGG id
BenjaSanchez Apr 27, 2020
4785040
fix-rxn: remove duplicated rxns
BenjaSanchez Apr 28, 2020
93d99ca
feat: BiGG dictionaries
BenjaSanchez Apr 29, 2020
6f593ef
fix-rxn.annot: correct reaction IDs and add new reaction IDs (MetaNet…
eiden309 May 16, 2020
48df2c6
fix-met.annot: correct metabolite IDs and add new metabolite IDs (Met…
eiden309 May 16, 2020
001c5a5
feat-rxn.annot: added new rxnKEGGIDs into model via ID mapping
eiden309 May 16, 2020
22eab97
feat-met.annot: added new metKEGGIDs into model via ID mapping
eiden309 May 16, 2020
ce55eeb
feat-met.annot: added new metMetaNetXID into model via ID mapping
eiden309 May 16, 2020
b3418ad
fix-met.annot: remove metabolite ID with modifyID.m and correct modif…
eiden309 May 16, 2020
76846e1
style: change notes annotation in modifyID.m to PR (#220)
eiden309 May 16, 2020
f0687d8
Update README.md
edkerk May 16, 2020
b3deb51
style-rxn.prop: shorten rxnNotes added in modifyID.m
eiden309 May 17, 2020
859e2ab
fix-rxn.annot: correct rxnName
eiden309 May 17, 2020
daa5737
style-met.prop: shorten metNotes added in modifyID.tsv
eiden309 May 17, 2020
029b34d
feat: add .gitattributes for unified line endings
eiden309 May 18, 2020
77906f8
fix: update .gitattributes
eiden309 May 19, 2020
682263d
fix: normalize all line endings
eiden309 May 19, 2020
b8a5d32
feat: add checks for MetaCyc/modelSEED data import in mapKEGGID.m
eiden309 May 19, 2020
80ff31a
fix: improve indexing in mapMNXMID.m
eiden309 May 19, 2020
f28c99f
Revert line endings commits
edkerk May 19, 2020
67a5b4e
feat: specify EOL behaviour in gitattributes
edkerk May 19, 2020
248d2be
Merge pull request #221 from SysBioChalmers/fix/normalizeLineEndings
edkerk May 19, 2020
eadc9f8
Merge remote-tracking branch 'origin/devel' into fix/update_IDs
edkerk May 19, 2020
24570ce
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez May 19, 2020
d21cae3
fix-data: split BiGG files in two separate lists
BenjaSanchez May 19, 2020
5132b88
fix-data: remove helper lists
BenjaSanchez May 19, 2020
cdbd689
fix-data: remove compartment info from met BiGG dict
BenjaSanchez May 19, 2020
e533f93
fix-data: keep original compartment abbreviations
BenjaSanchez May 19, 2020
ef49b1e
fix-data: automatic lipid id generation
BenjaSanchez May 19, 2020
71f8217
fix-data: manual lipid id curation
BenjaSanchez May 19, 2020
1987a59
fix-data: remove copy suffix from rxn BiGG dict
BenjaSanchez May 19, 2020
2d09bc9
style: minor formatting changes in mapKEGGID.m and mapMNXMID.m
eiden309 May 19, 2020
c41e0ec
fix: resolve issue with shortening rxnNotes and metNotes
eiden309 May 19, 2020
dc4ecc2
fix-data: redefine BiGG ids for SLIME rxns
BenjaSanchez May 20, 2020
5784e29
fix-data: exchange rxn notation in BiGG dict with new ids
BenjaSanchez May 20, 2020
d98fa22
fix-data: pseudo-mets & pseudo-rxns in both BiGG dicts
BenjaSanchez May 20, 2020
6290b49
fix: cd back to the original filefolder at the end
feiranl May 20, 2020
14a3b7b
Merge pull request #220 from SysBioChalmers/fix/update_IDs
BenjaSanchez May 20, 2020
0f2a766
fix-data: ER membrane notation in rxns
BenjaSanchez May 20, 2020
219203e
fix: changes to .gitignore
BenjaSanchez May 20, 2020
d35822e
fix-data: simple transport notation for rxn BiGG ids
BenjaSanchez May 20, 2020
87785e3
Merge branch 'devel' into feat/bigg_compliance
BenjaSanchez May 21, 2020
037c93f
fix-data: rename compartments in new rxn ids in BiGG dict
BenjaSanchez May 21, 2020
59b6d88
fix-data: misc manual fixes in new rxn BiGG dict
BenjaSanchez May 21, 2020
8a51b6f
fix-data: remove redundant chain position in new rxn BiGG dict
BenjaSanchez May 21, 2020
8ed678f
chore: update cobratoolbox/RAVEN
BenjaSanchez May 21, 2020
5ffdb0d
feat: met+rxn BiGG ids
BenjaSanchez May 25, 2020
7f72dea
feat: automatic curation of reactions via MetaNetX reac_prop.tsv
eiden309 May 26, 2020
89fb8a3
fix-rxn: balance reaction via modification of metabolite formula and …
eiden309 May 27, 2020
cd8a356
fix-rxn: balance reaction via modification of model.S
eiden309 May 27, 2020
35600d9
fix: remove requirement of coenzyme A in biomass equation for anaerob…
eiden309 May 27, 2020
8444355
Merge pull request #188 from SysBioChalmers/feat/bigg_compliance
BenjaSanchez May 27, 2020
1f7c113
Merge branch 'devel' into fix/unbalanced_rxns
BenjaSanchez May 27, 2020
e1d1945
feat: better python io functions
BenjaSanchez May 27, 2020
3963759
test: check if model changes with cobrapy
BenjaSanchez May 27, 2020
9469493
fix: cd to the right filefolder
feiranl May 27, 2020
a81a2cf
style: remove repetitive codes
feiranl May 27, 2020
8ccaa3e
feat: BiGG compliance flag in read_yeast_model
BenjaSanchez May 28, 2020
9b0ec0a
feat: load missing ids from bigg dicts
BenjaSanchez May 28, 2020
32e3391
fix: add exception for repeated BiGG ids
BenjaSanchez May 28, 2020
eb459aa
fix: revert back to original matlab-compliant model
BenjaSanchez May 28, 2020
60342ad
doc: add description for output
eiden309 May 29, 2020
53c81d9
fix: indexing issues when updating model.S
eiden309 May 29, 2020
17d84c9
fix: -R4 in TRX1
edkerk May 28, 2020
1979871
fix: resolve unbalanced rxns due to H+/H2O
eiden309 Jun 1, 2020
3941cde
fix-bug: mixed ID for MNXID and Notes
feiranl Jun 4, 2020
d3d7d71
fix: update with optimizeCbModel new output
feiranl Jun 4, 2020
57e0cab
fix-bug for wrong mets in the readme
feiranl Jun 5, 2020
afcb9fe
chore-cd to the right folder
feiranl Jun 5, 2020
e6205e9
feat-update the model with the balance of H+/H2O
feiranl Jun 5, 2020
15e6ccb
doc: rename to avoid conflict with COBRA function
eiden309 Jun 7, 2020
2ef9281
feat: display_rxnMetInfo.m to facilitate curation of reaction balance
eiden309 Jun 7, 2020
29181b9
feat: function to compile data for rxnDirection curation
eiden309 Jun 7, 2020
56b1295
feat: function and data to fix rxnDirection
eiden309 Jun 7, 2020
f976de9
fix: remove generic reaction r_4229
eiden309 Jun 7, 2020
984dca1
Merge pull request #224 from SysBioChalmers/feat/python-compatibility
BenjaSanchez Jun 10, 2020
39ada1b
Merge pull request #222 from SysBioChalmers/fix/unbalanced_rxns
BenjaSanchez Jun 12, 2020
9e36261
chore: update dependencies
BenjaSanchez Jun 12, 2020
0449d99
fix: gitignore conflict with master
BenjaSanchez Jun 15, 2020
e22f62f
fix: avoid binaries
BenjaSanchez Jun 15, 2020
4a8960d
fix: .gitattributes
BenjaSanchez Jun 15, 2020
c5b0d64
fix: remove authorships in scripts
BenjaSanchez Jun 18, 2020
c82e696
fix: update the missing BIGG IDs here in the notes part and also remo…
feiranl Jun 19, 2020
98b520d
feat-change model
feiranl Jun 19, 2020
ea3aafa
Merge remote-tracking branch 'origin/devel' into fix/reaction_direction
edkerk Jun 20, 2020
fb62634
refactor: remake models after merging devel
edkerk Jun 20, 2020
e17e007
Merge pull request #230 from SysBioChalmers/fix/remove-authorships
edkerk Jun 20, 2020
ce05769
Merge branch 'devel' into fix-MNXbug
BenjaSanchez Jun 22, 2020
af02d9a
Merge pull request #226 from SysBioChalmers/fix-MNXbug
BenjaSanchez Jun 23, 2020
152e6aa
Merge branch 'devel' into fix/reaction_direction
BenjaSanchez Jun 23, 2020
b49f192
doc: clarify Zenodo authorships
BenjaSanchez Jun 25, 2020
c1a34dc
doc: misc releasing guidelines
BenjaSanchez Jun 25, 2020
fb2523c
Merge pull request #233 from SysBioChalmers/fix/releasing-guidelines
BenjaSanchez Jun 26, 2020
b8d1747
fix: list of NTP reactions
eiden309 Jun 28, 2020
1ba4356
feat: create requirements via pip-tools
BenjaSanchez Jul 2, 2020
88e1668
feat: dev-requirements
BenjaSanchez Jul 2, 2020
02032da
feat: switch to touch for creating .env
BenjaSanchez Jul 3, 2020
3bf7462
refactor: simplify dev-requirements.in
BenjaSanchez Jul 3, 2020
fcd8771
doc: managing python dependencies
BenjaSanchez Jul 3, 2020
5d0d311
Merge pull request #235 from SysBioChalmers/feat/pip-tools
BenjaSanchez Jul 6, 2020
e9b8ef1
feat: add yaml validation
mihai-sysbio Jul 15, 2020
03d3007
fix-rxn: change dubious metabolite name
edkerk Jul 15, 2020
4c5888e
fix-rxn: r_0241 correct cofactor
edkerk Jul 15, 2020
cd1bae2
fix-rxn: r_0774 and r_0775 involve ATP hydrolysis
edkerk Jul 15, 2020
23d9218
fix-rxn: remove incorrect gene and EC number
edkerk Jul 15, 2020
0e3253a
Merge pull request #237 from SysBioChalmers/fix/misc
edkerk Jul 16, 2020
72e1c79
refactor: rely on ci-requirements
mihai-sysbio Jul 16, 2020
32d7e71
Merge branch 'feat/yaml-validation' into feat/memote
mihai-sysbio Jul 16, 2020
c96cc1c
feat: from travis to gh actions
mihai-sysbio Jul 16, 2020
cfe0db4
refactor: use second repo instance
mihai-sysbio Jul 17, 2020
efce14c
feat: remove travis integration
mihai-sysbio Jul 17, 2020
630abcd
feat: allow workflow to fail on error
mihai-sysbio Jul 17, 2020
fb8533a
feat: split memote workflow
mihai-sysbio Jul 17, 2020
975a27b
doc: visualization instructions
BenjaSanchez Jul 17, 2020
2594673
feat: memote workflow converts model, uses solver time limit
mihai-sysbio Jul 17, 2020
876ecce
fix: make sure .env exists
mihai-sysbio Jul 17, 2020
2f434f1
feat: add badge for memote history action
mihai-sysbio Jul 17, 2020
9979fcd
doc: correct metabolic atlas links
BenjaSanchez Jul 17, 2020
cd65a6a
Merge pull request #240 from SysBioChalmers/doc/yeast-gem-viz
BenjaSanchez Jul 17, 2020
a612772
chore: update dependencies
BenjaSanchez Jul 17, 2020
b09da06
fix-data: update rxnDirectionInfo.tsv
eiden309 Jul 24, 2020
2a51f9d
fix-the model change after updating the NTP list
feiranl Jul 25, 2020
b6afcbf
Merge branch 'devel' into fix/reaction_direction
BenjaSanchez Jul 27, 2020
d6fe4e9
fix-data: modelSEED rxnDirection update in rxnDirectionInfo.tsv
eiden309 Jul 29, 2020
12626ff
fix-small bugs of switching to right folder
feiranl Aug 1, 2020
31823d1
fix-data: deltaG and revIdx update in rxnDirectionInfo.tsv
eiden309 Aug 5, 2020
ccb1103
fix-met comps of Ferricytochrome b5 and Ferrocytochrome b5 from er to…
feiranl Aug 7, 2020
cbb1255
feat: check if model can grow
BenjaSanchez Aug 10, 2020
b144cad
doc: saveYeastModel to RAVEN style
BenjaSanchez Aug 10, 2020
bcfe0d9
feat: check for aerobic & anaerobic growth
BenjaSanchez Aug 10, 2020
f413def
feat: display flag for sumBioMass
BenjaSanchez Aug 10, 2020
1e56686
feat: flag for either warning or error if no growth
BenjaSanchez Aug 10, 2020
a2d1de8
Merge pull request #243 from SysBioChalmers/fix-growth
BenjaSanchez Aug 10, 2020
8e795ba
Merge pull request #244 from SysBioChalmers/feat/growth-check
BenjaSanchez Aug 14, 2020
0097ea1
Merge branch 'devel' into fix/reaction_direction
feiranl Aug 17, 2020
2eac413
style: remove blank spaces from rxnDirectionInfo.tsv
eiden309 Aug 18, 2020
af94579
Merge pull request #228 from SysBioChalmers/fix/reaction_direction
BenjaSanchez Aug 21, 2020
61778a2
fix-script: Add_esters_and_fusel_alcohol_pathways
wtscott31 Aug 28, 2020
8dc7642
Merge branch 'fix/FAEsters_Addition' of https://github.com/wtscott31/…
wtscott31 Aug 28, 2020
826cb45
fix/new_Fatty_acid_esters
wtscott31 Sep 1, 2020
9935dae
fix/new_Fatty_acid_esters_2
wtscott31 Sep 1, 2020
a212425
Merge remote-tracking branch 'origin/devel' into fix/FAEsters_Addition
edkerk Sep 1, 2020
be69083
feat: apply code on newest devel model
edkerk Sep 1, 2020
6f82d8a
fix: do not replace existing geneNames
edkerk Sep 1, 2020
b41004c
Merge pull request #190 from wtscott31/fix/FAEsters_Addition
edkerk Sep 2, 2020
86ad314
fix-rxn: remove non-compliant character
BenjaSanchez Sep 4, 2020
b63d4f5
fix-data: misc format
BenjaSanchez Sep 4, 2020
4f36a99
fix-data: delete compartment info from met file
BenjaSanchez Sep 4, 2020
9ff85ff
fix-data: delete repeats in met file
BenjaSanchez Sep 4, 2020
c0b1113
feat-met.prop: missing fields
BenjaSanchez Sep 4, 2020
f13e975
feat-met.annot: ChEBI & KEGG ids
BenjaSanchez Sep 4, 2020
44fdea6
fix: met/rxn notes
BenjaSanchez Sep 4, 2020
7af6f37
feat-rxn.annot: subSystems
BenjaSanchez Sep 4, 2020
a84b0c5
fix: correct metFormula and rxn stoichiometry
edkerk Sep 4, 2020
014c2a6
fix: remove duplicate reaction
edkerk Sep 4, 2020
2e0a63a
fix-rxn: delete rxn with dead-end met
BenjaSanchez Sep 18, 2020
6094f32
Merge pull request #248 from SysBioChalmers/fix/fa-esters-addition
BenjaSanchez Sep 21, 2020
da3d35e
fix-rxn.annot: combine glycolysis + gluconeogenesis
BenjaSanchez Oct 5, 2020
27350d4
Merge pull request #251 from SysBioChalmers/fix/gluconeogenesis
BenjaSanchez Oct 6, 2020
a49721c
chore: update COBRA
BenjaSanchez Nov 23, 2020
b2f3d69
chore: update RAVEN
BenjaSanchez Nov 23, 2020
41be91c
chore-rxn: move KEGG pathway ids to proper field
BenjaSanchez Nov 24, 2020
d28afbe
Merge pull request #253 from SysBioChalmers/chore/update-toolboxes
BenjaSanchez Nov 25, 2020
5e16d26
fix-rxn/met: solves #252 and #254
edkerk Apr 6, 2021
3a90310
Merge branch 'devel' into feat/yaml-validation
mihai-sysbio Apr 7, 2021
56874b0
fix: deal with special characters in README.md
edkerk Apr 7, 2021
1d5b325
fix: valid yaml
edkerk Apr 9, 2021
122dc3f
Merge branch 'fix/various' into feat/yaml-validation
mihai-sysbio Apr 10, 2021
a3497b4
Merge pull request #236 from mihai-sysbio/feat/yaml-validation
edkerk Apr 10, 2021
9dc7203
chore: update *requirements.txt
edkerk Apr 10, 2021
61976a5
Merge branch 'devel' into feat/memote
mihai-sysbio Apr 11, 2021
5cab2ba
fix: missisng ci-requirements
mihai-sysbio Apr 11, 2021
078be53
Merge branch 'fix/requirements' into feat/memote
mihai-sysbio Apr 11, 2021
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5 changes: 5 additions & 0 deletions .gitattributes
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
* text=auto
*.m text diff=matlab
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
55 changes: 41 additions & 14 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,23 +41,26 @@ Here's how to set up yeast-GEM for local development to contribute smaller featu
```
git clone https://github.com/<your Github name>/yeast-GEM.git
```

4. Check out the branch that you want to contribute to. Most likely that will be ``devel``:
```
git checkout devel
```

5. Create a branch for local development based on the previously checked out branch ([see below](#branching-model) for details on the branching model and how to name your branch):
```
git checkout -b name-of-your-branch
```

6. Now you can make your changes locally!
* Always make your changes in Matlab and never directly editing the model files. For loading the model use `loadYeastModel.m`, and for saving the model use `saveYeastModel.m`. The latter will ensure all 3 versions of the model (`.xml`, `.yml` & `.txt`) get updated in the same way.
* If your changes are minor (e.g. a single chemical formula you wish to correct), you can do it directly from the command line.
* If your changes are not so small and require several steps, create a script that loads the model, reads data (if applicable), changes the model accordingly, and saves the model back.
* Each script should start with a commented section describing the script, explaining the parameters, and indicating your name and the date it was written. Existing functions can clarify what style should be used.
* If you add new metabolites and/or rxns to the model, please use `/ComplementaryScripts/otherChanges/getNewIndex.m` for obtaining new ids. If you add a new gene, please use as id the [systematic names from SGD](http://seq.yeastgenome.org/help/community/nomenclature-conventions).
* As much as possible follow the model conventions:
- For new metabolites and/or reactions, please use `/ComplementaryScripts/otherChanges/getNewIndex.m` for obtaining new ids.
- For metabolite and/or reaction names, please avoid any unconventional characters (e.g. Greek letters).
- For new genes, please use as id the [systematic names from SGD](http://seq.yeastgenome.org/help/community/nomenclature-conventions).
* Store scripts in the appropriate folder in `/ComplementaryScripts` and data (as `.tsv` files) in the appropriate folder in `/ComplementaryData`. If you think no folder is adequate for your script/data, feel free to create your own folder. Note that binary data such as `.mat` structures or `.xls` tables cannot be stored in the repo (as they cannot be version-controlled, and they increment too much the size of the repo).
* When you are done making changes, review locally your changes with `git diff` or any git client, to make sure you are modifying the model as you intended.

Expand Down Expand Up @@ -86,7 +89,7 @@ Thank you very much for contributing to yeast-GEM!
* `gh-pages`: Is only touched by the administrator and for maintaining the [landing page](http://sysbiochalmers.github.io/yeast-GEM/) of yeast-GEM.

* `{chore, doc, feat, fix, refactor, style}/descriptive-name`: Any other branch created in the model. If you work on a fix, start the branch name with `fix/`, if you work on a feature, start the branch name with `feat/`. Examples: `fix/format_reactions` or `feat/new_algorithms`. [See below](#semantic-commits) for more details on the possible actions you can use.

#### Semantic commits

Please use concise descriptive commit messages. Ideally, use semantic commit messages to make it easier to show what you are aiming to do:
Expand All @@ -95,7 +98,7 @@ Please use concise descriptive commit messages. Ideally, use semantic commit mes
* `action` = {`feat`, `fix`, `refactor`, `style`, `doc`, `chore`, `test`}
* `object` (optional field) = {`rxn`, `rxn.annot`, `rxn.prop`, `met`, `met.annot`, `met.prop`, `gene`, `gene.annot`, `comp`, `comp.annot`, `data`}

`action` refers to what exactly are you doing in the commit, following a [standard definition](http://karma-runner.github.io/2.0/dev/git-commit-msg.html) in software development:
`action` refers to what exactly are you doing in the commit, following a [standard definition](http://karma-runner.github.io/2.0/dev/git-commit-msg.html) in software development:
* `chore`: updating toolbox, data files, etc.
* `doc`: updating documentation or explanatory comments in functions.
* `feat`: new feature added, e.g. new reaction / metabolite / function / etc.
Expand Down Expand Up @@ -143,7 +146,7 @@ Follow all other steps in the same way. Also, when creating your pull request (o
* Choose 1 or more members of the team (ideally with knowledge on the pull request) as reviewers. Note that the person making the pull request and the reviewer _cannot_ be the same person.
* Assign appropriate [labels](https://github.com/SysBioChalmers/yeast-GEM/issues/labels).
* Assign the pull request to one of the available [projects](https://github.com/SysBioChalmers/yeast-GEM/projects), if applicable.

### Reviewing pull requests

Every pull request must be approved by at least one reviewer before it can be merged. When reviewing someone else's pull request, keep in mind the following aspects:
Expand All @@ -160,6 +163,7 @@ Every pull request must be approved by at least one reviewer before it can be me
This section is meant for the administrator of this repo. The main duties of the administrator are:
* To make sure conventions and standards in the model are kept.
* To keep the repository clean and organized, i.e. avoid redundancy in functions and/or data, and keep coherency in naming of files.
* To manage package dependencies and regularly update them.
* To help in the reviewing process of external pull requests by assigning reviewers, [labels](https://github.com/SysBioChalmers/yeast-GEM/issues/labels) and [projects](https://github.com/SysBioChalmers/yeast-GEM/projects), if applicable.
* To keep [issues](https://github.com/SysBioChalmers/yeast-GEM/issues) with the proper labels, and to close them once they are fixed in the `master` branch.
* In cases of disagreement between contributors, to decide how to resolve the issue.
Expand All @@ -172,6 +176,21 @@ The following points should be considered when merging branches to `devel`:
* Wait at least a day before merging, to allow other developers to inspect the pull request.
* As soon as the branch is merged, check if `devel` is still possible to merge to `master` (this can be checked [here](https://github.com/SysBioChalmers/yeast-GEM/compare/devel)). If conflicts appear (which should rarely happen and only if the `.xml` file was changed in an unexpected way by a toolbox update), fix the conflict _locally_ as soon as possible in `devel` and then push it (note, **DO NOT** pull any other changes from `master` to `devel`, just the single file that is creating the conflict).

### Managing python dependencies

We use [pip-tools](https://github.com/jazzband/pip-tools) for managing dependencies:

* If a new dependency is needed for users/developers:
1. Add the dependency to `/requirements/requirements.in` or `/requirements/dev-requirements.in`, respectively (note that by default any requirement in `requirements.in` will also be in `dev-requirements.in`).
2. From `/requirements`, run `pip-compile requirements.in` and/or `pip-compile dev-requirements.in` as needed.

* If dependencies need to be upgraded, from `/requirements` run:
```
pip-compile --upgrade requirements.in
pip-compile --upgrade dev-requirements.in
```
Dependencies should be upgraded regularly, but always first tested in separate branches.

### Releasing a new version

* A merge of `devel` with `master` invokes a new release.
Expand All @@ -190,17 +209,25 @@ yeast-GEM follows [semantic versioning](https://semver.org/), adapted to GEMs:
* Updating toolboxes.
* Re-organization of data
* Refactoring of code.

When releasing, please follow these steps:
1. Make sure all dependencies in `devel` correspond to the setup from the local computer from which the release will be made. If not, make a single commit in `devel` updating this with a `loadYeastModel`/`saveYeastModel` cycle.
2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Fixes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Closes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
3. Merge at least a day after (having at least one accepted review).
4. Switch locally to `master` and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
4. Switch locally to `master`, pull changes and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
5. Bump version with `increaseVersion.m`. **NOTE:** The function will error if unexpected changes are occurring. If this happens, probably step 1 was done incorrectly. To fix it, commit in `devel` any necessary changes and make a new pull request.
6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`.
7. Make the new release at GitHub (https://github.com/SysBioChalmers/yeast-GEM/releases/new), using the proper tag "vX.Y.Z" and with the same description as the corresponding PR from step 2.
8. Pull from `master` to `gh-pages` to update the landing page.

6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`, and push to the remote.
7. Make the new release at GitHub [here](https://github.com/SysBioChalmers/yeast-GEM/releases/new), using the proper tag "vX.Y.Z" and with the same description as the corresponding PR from step 2.
8. Merge locally `master` into `gh-pages` and push to update the landing page.
9. Review the [Zenodo](https://zenodo.org) release: Every new release from Github (step 7) automatically triggers a new release in Zenodo. However, so far it is not possible to fully customize this release, and some manual curation is needed. This includes:
* Ensuring the title of the release has the format `SysBioChalmers/yeast-GEM: yeast X.Y.Z`.
* Correcting author names to include all commit authors and PR reviewers that contributed to the release.
* Ensuring the version of the release has the format `vX.Y.Z`.
* Setting the language to English.
* Adding any grant IDs (if applicable).

Make sure to both save & publish your edits. You will find the new release at the top of [all Zenodo releases](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%221494182%22&sort=-publication_date&all_versions=True). Note that it might take some minutes for the Zenodo release to appear after you create the release in Github.

## Acknowledgments

These contribution guidelines were written based on the contribution guidelines of [opencobra/cobrapy](https://github.com/opencobra/cobrapy/blob/devel/.github/CONTRIBUTING.rst) and [SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN/wiki/DevGuidelines).
2 changes: 0 additions & 2 deletions .github/issue_template.md
Original file line number Diff line number Diff line change
Expand Up @@ -21,5 +21,3 @@
- [ ] Done this analysis in the `master` branch of the repository
- [ ] Checked that a similar issue does not exist already
- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue

*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*
2 changes: 0 additions & 2 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,3 @@
- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---contributor) for running the model
- [ ] Selected `devel` as a target branch (top left drop-down menu)
- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about this PR

*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*
53 changes: 53 additions & 0 deletions .github/workflows/memote-history.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
name: Memote history

on: push

jobs:
memote-history:
runs-on: ubuntu-latest
steps:

- name: Checkout
uses: actions/checkout@v2
with:
fetch-depth: 0

- name: Set up Python 3
uses: actions/setup-python@v2
with:
python-version: '3.x'

- name: Install memote
run: pip install -r requirements/ci-requirements.txt

- name: Setup variables
id: setup
run: |
echo "::set-output name=history::history_report.html"
echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
echo "::set-output name=location::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /location/) print $2}' memote.ini | tr -d ' ')"
echo "::set-output name=other-repo::gh-pages-repo"

- name: Checkout repo for gh-pages branch
uses: actions/checkout@v2
with:
repository: ${{ github.repository }}
ref: ${{ steps.setup.outputs.deployment }}
path: ${{ steps.setup.outputs.other-repo }}

- name: Memote on push
run: |
memote run --skip-unchanged
# Generate the history report on the deployment branch
memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"

- name: Auto-commit results
uses: stefanzweifel/[email protected]
with:
commit_user_name: memote-bot
commit_message: update memote history report
file_pattern: ${{ steps.setup.outputs.history }}
branch: ${{ steps.setup.outputs.deployment }}
repository: ${{ steps.setup.outputs.other-repo }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
24 changes: 24 additions & 0 deletions .github/workflows/memote-run.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
name: Memote history

on: pull_request

jobs:
memote-run:
runs-on: ubuntu-latest
steps:

- name: Checkout
uses: actions/checkout@v2

- name: Set up Python 3
uses: actions/setup-python@v2
with:
python-version: '3.x'

- name: Install memote
run: pip install -r requirements/ci-requirements.txt

- name: Memote on PR
run: |
# Untracked build, skip saving to gh-pages
memote run --ignore-git
41 changes: 41 additions & 0 deletions .github/workflows/yaml-validation.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
name: YAML validation

on:
push:
branches: [ devel ]
pull_request:
branches: [ master, devel ]

jobs:
yaml-validation:
runs-on: ubuntu-latest
steps:

- name: Checkout
uses: actions/checkout@v2
with:
fetch-depth: 1

- name: YAML Lint
uses: ibiqlik/[email protected]
continue-on-error: true
with:
## File(s) or Directory, separate by space if multiple files or folder are specified
file_or_dir: ModelFiles/
## Custom configuration (as YAML source)
config_data: "{extends: default, rules: {line-length: disable}}"
## Format for parsing output [parsable,standard,colored,auto]
# format: # optional, default is colored
## Return non-zero exit code on warnings as well as errors
# strict: # optional, default is false

- name: Set up Python 3
uses: actions/setup-python@v2
with:
python-version: '3.x'

- name: Import with cobrapy
continue-on-error: true
run: |
pip install -r requirements/ci-requirements.txt
python -c "import cobra ; cobra.io.load_yaml_model('ModelFiles/yml/yeastGEM.yml')"
10 changes: 8 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -41,13 +41,19 @@ Thumbs.db
*.asv
*.m~
*.mex*
*.mlappinstall
*.mlappinstall
*.mltbx
*.mat
helpsearch*/

# Python-related things #
#########################
*.ipynb_checkpoints/
*.pyc
*.env

# Non-complying tables #
########################
*.xls
*.xlsx
*.tab
*.tab
16 changes: 0 additions & 16 deletions .travis.yml

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