Skip to content

RESTART - only MFA #13

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mmattano wants to merge 52 commits into
base: master
Choose a base branch
from
Open

RESTART - only MFA #13

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
52 commits
Select commit Hold shift + click to select a range
d231cd1
Merge pull request #1 from AutoFlowResearch/develop
mmattano Jan 12, 2021
3dad6e9
Merge pull request #2 from AutoFlowResearch/develop
mmattano Jan 28, 2021
bf2af07
Merge pull request #4 from AutoFlowResearch/develop
mmattano Mar 10, 2021
e23efea
Merge pull request #7 from AutoFlowResearch/develop
mmattano Mar 31, 2021
ac7258b
Merge pull request #8 from AutoFlowResearch/develop
mmattano Apr 16, 2021
30ce9f3
Merge branch 'AutoFlowResearch:develop' into develop
mmattano Jun 3, 2021
fdc3237
Merge pull request #12 from mmattano/master
mmattano Feb 1, 2022
45fff02
RESTART - only MFA
mmattano Feb 1, 2022
4326ce4
Update config.yml
mmattano Feb 1, 2022
5ef4007
Update requirements.txt
mmattano Feb 1, 2022
9991aae
Removed unnecessary tests
mmattano Feb 1, 2022
7db9642
Changed now missing dependency
mmattano Feb 1, 2022
24e1a19
deleted C1, C2 etc
v-saad Mar 14, 2022
1540502
outcommented f = estimate
v-saad Mar 22, 2022
8f37792
minor changes
v-saad Apr 24, 2022
ac45c4c
fix: changed mdv to idv
v-saad Apr 28, 2022
2aaaaa8
updated mdv to idv
v-saad Apr 28, 2022
80d88f7
Merge pull request #1 from mmattano/develop
v-saad Apr 28, 2022
8e20a7a
changed test file
v-saad Apr 28, 2022
7f94bf5
Merge branch 'branch3' of https://github.com/v-saad/AutoFlow-OmicsDat…
v-saad Apr 28, 2022
20f06be
Merge pull request #14 from v-saad/branch3
mmattano Apr 28, 2022
7db36e9
feat: create folder for parsers and add INCA reaction parser
v-saad Jun 29, 2022
7eec8c3
Update README.md
v-saad Jun 29, 2022
b5b03f5
Merge pull request #16 from v-saad/Parser-stage02
mmattano Jul 11, 2022
065c572
Merge pull request #15 from v-saad/patch-1
mmattano Jul 11, 2022
385a63f
fix: update to INCA 2.0
mmattano Jul 11, 2022
0bb997e
fix: clean up files
mmattano Jul 11, 2022
30c9745
Update env.yml
mmattano Jul 11, 2022
8f40908
fix: changed to follow pandas update
mmattano Jul 11, 2022
02b1321
fix: downgraded to prevent issue with Escher
mmattano Jul 11, 2022
e5af2de
Update distributions.py
mmattano Jul 11, 2022
45751f7
Changes/fixes dump
mmattano Dec 23, 2022
a7b2e05
and some more
mmattano Dec 23, 2022
4bdafeb
refactor: combine_duplicated_compounds
viktorht Dec 27, 2022
9bdfa8d
Generalises handling of filepaths.
viktorht Jan 5, 2023
9ac1c2f
Merge branch 'refactor_data_import_parsers' into develop
viktorht Jan 5, 2023
982d77a
Corrected mistake in error message
viktorht Jan 9, 2023
4600515
Produce the model configuration files for simple test model
viktorht Jan 9, 2023
60be804
Reorganized test files
viktorht Jan 9, 2023
b6a8feb
Created measurements file with data from the INCA simple model demo
viktorht Jan 9, 2023
70156cb
Created tracers.csv with tracer from INCA simple model demo
viktorht Jan 9, 2023
3f93c18
Ignores pytest.ini
viktorht Jan 9, 2023
4b93439
Fluxes measurement based on the simple model demo
viktorht Jan 9, 2023
4b4a93e
Test add_reaction_to_script and add_reaction_parameters methods with …
viktorht Jan 9, 2023
867c9af
Testing .add_experimental_parameters() and .script_generator() methods
viktorht Jan 11, 2023
b7b5ff0
Created fixture and test for symmetrical_metabolites() method
viktorht Jan 12, 2023
d0751fb
tests .mapping() method
viktorht Jan 12, 2023
80079dc
tests that mapping can parse multiple experiments
viktorht Jan 12, 2023
58e7fbe
Generates the INCA script and runs the simple test model in INCA
viktorht Jan 12, 2023
bcd4929
Merge pull request #17 from viktorht/refactor_data_import_parsers
viktorht Jan 12, 2023
41201b7
Merge pull request #18 from viktorht/update_filepath_handling
viktorht Jan 12, 2023
dc4c6f6
Merge pull request #21 from viktorht/simple_test_model
viktorht Jan 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .circleci/config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ version: 2.1

orbs:
win: circleci/windows@2.2.0
linux: cloudesire/openjdk-install@1.2.3
#linux: cloudesire/openjdk-install@1.2.3

commands:
install-conda:
Expand Down
4 changes: 4 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ coverage.xml
*.py,cover
.hypothesis/
.pytest_cache/
pytest.ini

# Translations
*.mo
Expand Down Expand Up @@ -140,3 +141,6 @@ dmypy.json

# Pyre type checker
.pyre/

# Mac
.DS_Store
Loading