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Merging changes from Martin's (althonos) repo to Tom's (tomnl) #2

Merged
merged 135 commits into from
Oct 25, 2016
Merged

Merging changes from Martin's (althonos) repo to Tom's (tomnl) #2

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6a8fe45
Added Python3 support. Moved install process from distutils to setupt…
althonos Jun 3, 2016
fad3dfb
Corrected examples.py to work with both Python versions. Added syntax…
althonos Jun 3, 2016
298639a
Changed xpaths to work with a broader spectrum of formats. Started te…
althonos Jun 3, 2016
67c33be
Refactored xpaths expressions. Standardized the use of .attrib[] acce…
althonos Jun 6, 2016
c663c58
Added metabolights.sh (requires curlftpfs) bash script to test mzml2i…
althonos Jun 7, 2016
67ed0f9
Added some more try/except for files lacking some fields (see scripts…
althonos Jun 7, 2016
c41c5ca
Separated values parsing into different functions. Accession numbers …
althonos Jun 8, 2016
a904991
Updated documentation
althonos Jun 8, 2016
a316ab4
Corrected some issues with code (hardcoded path, not replacing the ri…
althonos Jun 8, 2016
e28b9c2
Added a check so that parser shouldn't parse empty studies and fail r…
althonos Jun 8, 2016
6bd93e0
Modified metabolights.sh so that already generated ISA studies are no…
althonos Jun 9, 2016
e8455dc
Changed template isa assay to work with default ISACreator configurat…
althonos Jun 9, 2016
3595af6
Added warning system for impossible to parse / absent values.
althonos Jun 10, 2016
5e53680
Added warning system. Tweaked behaviour for the sake of GUI compatibi…
althonos Jun 10, 2016
08e4c17
Added more options for templating engine.
althonos Jun 13, 2016
0cd87d7
Tweaks
althonos Jun 13, 2016
95c1a1a
Added an option to split assays depending on the polarity.
althonos Jun 14, 2016
03daf60
Made slight changes to templating engine. Added a progress bar to cli.
althonos Jun 16, 2016
4e57dbb
Moved lxml and progressbar to extra dependencies.
althonos Jun 16, 2016
43707c5
Updated readme.
althonos Jun 17, 2016
5b179cf
Minor fixes to work better with mzml2isa-qt.
althonos Jun 22, 2016
f977a3d
Fixed a case of linked dict & list which broke contacts roles ontology.
althonos Jun 22, 2016
d245148
Reverted to earlier version of template file.
althonos Jun 23, 2016
c4f1fd9
Tweaked to increase support for imzML files. Removed unnecessary colu…
althonos Jun 24, 2016
57477dd
Slightly changed warnings & assay template data
althonos Jun 24, 2016
1a00237
Reinforced support for imzml.
althonos Jun 28, 2016
5128aec
Changed build_env to fit with both mzML and imzML. Added an executabl…
althonos Jun 30, 2016
21fa09e
Added TravisCI integration and tests on MetaboLights database.
althonos Jul 3, 2016
c4fad54
Modified scripts/metabolights.sh to work with Travis.
althonos Jul 3, 2016
0d9dd45
Removed useless scripts.
althonos Jul 3, 2016
de2404a
Corrected issue with curlftpfs.
althonos Jul 3, 2016
523c492
Removed Py2 from Travis tests and parallelized MetaboLights studies p…
althonos Jul 3, 2016
dbe864a
Added multiprocessing option to command line app.
althonos Jul 3, 2016
fdbb079
Ported program to work with pronto library.
Jul 4, 2016
11f6937
Added GPLv3 to setup.py classifiers.
Jul 4, 2016
eddce7e
Removed MTBLS studies that took too long for Travis jobs.
Jul 4, 2016
08b4c08
Instantiate a single Ontology.
Jul 4, 2016
6e91c9d
Rewrote some parts of mzml.py and parsing.py. Updated README.rst.
Jul 5, 2016
6b8a763
Corrected an ontology import issue. Added software version & checksum…
Jul 6, 2016
f75ceeb
Changed scan polarity values to be more compliant with MetaboLights I…
Jul 7, 2016
99548ce
Changed ontology location for imagingMS.obo (www.maldi-msi.org)
Jul 7, 2016
96c6427
Added an ISA validation step to the Travis CI tests.
Jul 7, 2016
27e2a7e
Changed ISA-Tab formatting to "{}.format('mustache')" python formatti…
Jul 7, 2016
fe2fa99
Corrected a case of overwriting headers with multiple value headers. …
Jul 7, 2016
6a2977c
Corrected a case of overwriting headers with multiple value headers. …
Jul 7, 2016
03ddd6b
Reworked assay templating.
Jul 7, 2016
5a4e8ca
Improved ISA generated files. Started mapping parameters with CV.
Jul 7, 2016
ab4258d
Tweaked templates & .travis.yml
Jul 7, 2016
e1253b6
Corrected a failing case when no instruments are extracted.
Jul 7, 2016
6370602
Fixed Py2 dependencies.
Jul 8, 2016
7a08f03
Added templates for imzML. Corrected validation error.
Jul 8, 2016
646f5b1
Changed template file.
Jul 8, 2016
7232438
Added an ISA validation step to the Travis CI tests.
Jul 7, 2016
32fdaea
Added comment to add version of mzml2isa used to produce ISA-Tab files.
Jul 8, 2016
2596246
Fixed .travis.yml
Jul 8, 2016
abeb80b
Reimplemented multipolarity assay generation
Jul 9, 2016
3c78c39
Corrected a failing case. Reverted to mzml2isa-qt compliant ISA forma…
Jul 11, 2016
372ac5d
Fixed study template for imzML
Jul 11, 2016
f79aff6
Reimplemented multiple contacts support.
Jul 11, 2016
edc64c3
Fixed crash during ISA writing when no instrument was found
Jul 11, 2016
a19d027
Changed validation to use current isa-api validator
Jul 11, 2016
cfcadea
Removed unnecessary print. Cleaned travis.yml.
Jul 12, 2016
7856b5c
Added requirements.txt. Reverted to java validation as isa-api does n…
Jul 12, 2016
93eb112
Corrected issue in i_imzML.txt
Jul 12, 2016
7a91f12
Merge branch 'mustache'
Jul 12, 2016
7e6df12
Fixed travis + lxml
Jul 12, 2016
b24a372
Added --version argument to CLI.
Jul 13, 2016
a98b921
Added doc badge and removed info redundant with documentation, provid…
Jul 13, 2016
9f6a17a
Fixed case of variable which caused it not to be extracted [skip ci]
Jul 13, 2016
d3c21a0
Fixed Binary Checksum for imzML to extract value as well [ci skip].
Jul 13, 2016
86e07e8
Added unit extraction to time range and m/z range. Added urlization t…
Jul 14, 2016
ade8058
De-listed Detector mode.
Jul 14, 2016
3b5732b
Fixed image search for imzml (now relays on identity % to file name)
Jul 14, 2016
44d4c74
Added scan polarity extraction for imzML. Added cv term for polarity …
Jul 14, 2016
118b088
Fixed a_imzML.txt (in Detector mode ref&accession field) [ci skip]
Jul 14, 2016
c5610c8
Added an Identity threshold to the identification of high-res and low…
Jul 14, 2016
447596e
Enriched imzML template. [ci skip]
Jul 14, 2016
2cc44c0
Allowed merged spectra to display both Spectrum Representation.
Jul 14, 2016
dbcdb55
Removed MTBLS228 and MTBLS273 from allowed failures
Jul 14, 2016
6082769
Fixed solvent displaying wrong ontology ref & accession for imzML.
Jul 14, 2016
1db5564
Relevant values are now of int and float type instead of always being…
Jul 14, 2016
e5f2b41
Relevant values are now of int and float type instead of always being…
Jul 14, 2016
330c8b4
Added scan-level metadata extraction.
Jul 15, 2016
9f6eeb2
Fixed polarity
Jul 15, 2016
cf2f6eb
Made performance enhancements (memoization of descendents in cvParam_…
Jul 15, 2016
ef66bd7
Change warnings to be displayed once. Removed traceback from warnings.
Jul 15, 2016
73c9d4d
Remove references to unused code in README
Jul 18, 2016
afb400c
Fix py2 requirements not being included in sdist [ci skip]
Jul 18, 2016
ee3dc76
Replace find_all with iterfind. Change tree parsing to iterparse
Jul 19, 2016
3c80585
Fix minor performance issues
Jul 19, 2016
059a4c0
Remove pymzml references
Jul 20, 2016
ad3ecd0
Merge branch 'experimental'
Jul 21, 2016
87db05d
Fix merge issue
Jul 21, 2016
23764f5
Fix if condition raising warning all the time
Jul 21, 2016
9255a89
Add MTBLS341 to tests
Jul 21, 2016
d7f062e
Make mzml2isa able to parse zip tar/tar.gz folders. Make usermeta rea…
Tomnl Jul 22, 2016
cc96bee
Fix indentation & generator issues
Jul 22, 2016
59a1f7c
Fix StopIteration not being caught in derived
Jul 26, 2016
53188d3
Remove Py2 tests to speed up builds
Jul 26, 2016
456494d
Remove Py2 tests to speed up builds
Jul 26, 2016
e1b3955
Merge branch 'ziptar'
Jul 26, 2016
a165b40
Fix sh**ty merge
Jul 26, 2016
a3f7322
Fix .tar.gz extraction
Jul 26, 2016
a2e4330
Fix template [ci skip]
Jul 26, 2016
889de19
Fix failing case for imzML
Jul 26, 2016
fbf9009
Fix unit extraction for timerange. Remove CV of serial number
Jul 26, 2016
c53e693
Fix crash case
Jul 27, 2016
d22c544
Fix issue with Waters files
Jul 27, 2016
9a3f4d5
Remove deploy from Travis [ci skip]
Jul 28, 2016
87715ed
Add DOI badge to README [ci skip]
Jul 28, 2016
5d3c917
Update README.rst
rsalek Aug 11, 2016
f163ef6
Update README.rst
rsalek Aug 11, 2016
0c3fd9e
Update README.rst
rsalek Aug 11, 2016
3a7b344
Update README.rst
rsalek Aug 11, 2016
4a778a9
Enhanced doc [ci skip]
Aug 11, 2016
78657be
Removed argparse requirement
Aug 11, 2016
506b990
Merge branch 'master' of https://github.com/althonos/mzml2isa
Aug 11, 2016
5535899
Release v0.4.23
Aug 11, 2016
5821374
Edit MANIFEST.in [ci skip]
Aug 12, 2016
6ee8907
Add warnings and try/except to usermeta json parsing
Aug 16, 2016
c08a71e
Update workflow graph on README page [ci skip]
Aug 16, 2016
02c13ff
Add bioconda badge
RJMW Aug 17, 2016
b8ac492
Merge pull request #14 from RJMW/add-bioconda-badge
althonos Aug 17, 2016
b9ddd56
Change bioconda badge style to flat [ci skip]
Aug 17, 2016
a4de393
Update ontology files to latest available versions
Sep 14, 2016
e79eedf
Quote unquoted ontology description entry
Sep 28, 2016
6454784
Map Source name in study templates to Sample Name
Sep 28, 2016
dec1ba6
Fix multiple line breaks on windows
Sep 28, 2016
ddc282c
Fix ontology importing
Sep 28, 2016
dbb7dcd
Release v0.4.26
Sep 28, 2016
2362f6c
Fix imzML image file mapping and rename -M flag to -j (jobs)
Sep 28, 2016
6ba948b
Release v0.4.27
Sep 30, 2016
5e207c1
Attempt workaround to avoid long loading times
Oct 1, 2016
f14a8af
Release v0.4.28
Oct 1, 2016
7a01d92
Set default warning control level to once (fix #19)
Oct 25, 2016
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Update workflow graph on README page [ci skip]
  • Loading branch information
Martin Larralde committed Aug 16, 2016
commit c08a71eb81b6fb725a9c537d3f0dca62e51f2472
1 change: 1 addition & 0 deletions MANIFEST.in
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Expand Up @@ -2,3 +2,4 @@ include mzml2isa/*.obo
include mzml2isa/default/*.txt
include README.rst
include requirements*.txt
include isa_config/mzml2isa.png
2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -72,7 +72,7 @@ studies.
Workflow
--------

.. figure:: https://raw.githubusercontent.com/Tomnl/mzml2isa/master/isa_config/mzml2isa.png
.. figure:: isa_config/mzml2isa.png
:alt: workflow


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