Test Pull Request: (#20)

* Moved files to WormJam Core repo

* Website testing

* Set theme jekyll-theme-slate

* Initial Test of Travis CI

* Initial Test of Travis CI + added model files to curation directory

* Added requirements.txt

* Using 01 Aug 2019 version as draft breaks CI pipeline

* Fixed a text error in one of the tsv files.

* Fixed another text error in one of the tsv files.

* Changed the structure of the tests to give user better feedback

.travis.yml

@@ -0,0 +1,46 @@
+language: python
+python:
+   - "3.7"
+branches:
+  only:
+    - devel
+install:
+  - pip install -r requirements.txt
+jobs:
+  include:
+    - stage: build_model
+      script: python python/tsv_to_sbml.py
+    - stage: basic_tests
+      script:
+        - python python/tsv_to_sbml.py
+        - python python/basic_fba.py
+        - python python/restricted_fba.py
+    - stage: generate_report
+      script: 
+        - python python/tsv_to_sbml.py
+        - travis_wait 2 python python/basic_fba.py
+        - python python/restricted_fba.py
+        - if [ $TRAVIS_PULL_REQUEST != "false" ]; then
+            travis_retry memote run --ignore-git --location . test_model.xml >&1 | tee results.txt;
+            python python/comment_script.py $GITHUB_TOKEN $TRAVIS_REPO_SLUG $TRAVIS_PULL_REQUEST;
+          else
+            travis_retry memote report snapshot --filename "docs/report.html" test_model.xml;
+          fi
+        - python python/manage_reports.py
+
+stages:
+  - build_model
+  - basic_tests
+  - generate_report
+
+
+deploy:
+  - provider: pages
+    skip_cleanup: true
+    github_token: $GITHUB_TOKEN  # Set in the settings page of your repository, as a secure variable
+    keep_history: true
+    on:
+      branch: devel
+      condition: $TRAVIS_PYTHON_VERSION = "3.7"
+    target_branch: gh-pages
+

curation/Compartment-SBtab.tsv

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+!!SBtab SbtabVersion='1.0' TableType='Compartment' TableName='WormJam compartments'
+!ID	!Name	!Identifiers:go	!Comment
+c	Cytosol	GO:0005829	
+e	Extracellular	GO:0005576	This mix the extracellular and extra-organism compartments
+m	Mitochondrion	GO:0005739	
+n	Nucleus	GO:0005634	
+i	Mitochondrial Inner Membrane	GO:0005759	Added to segregate hydrogen for ATP production

curation/Compound-class-SBtab.tsv

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+!!SBtab SbtabVersion='1.0' TableType='Compound-class' TableName='Wormjam compound classes'
+!ID !Name   !Kind   !Identifiers:chebi  !Comment    !Curator

curation/Curator-SBtab.tsv

@@ -0,0 +1,20 @@
+!!SBtab SbtabVersion='1.0' TableType='Curator' TableName='Example of Curator list'
+!ID	!given-name	!family-name	!organization-name	!email
+lenov	Nicolas	Le Nov<e8>re	The Babraham Institute	[email protected]
+rodrigue	Nicolas	Rodriguez	The Babraham Institute	[email protected]
+janna	Janna	Hastings	The Babraham Institute	[email protected]
+wimi	Michael	Witting	Helmholtz Zentrum Munich	[email protected]
+hjs	Horst Joachim	Schirra	The University of Queensland	[email protected]
+nel	Nathan E	Lewis	University of California, San Diego	[email protected]
+abraham	Abraham	Mains	The Babraham Institute	[email protected]
+cjj	Chintan	Joshi	University of California, San Diego	[email protected]
+pre	Paul	Ebert	The University of Queensland	[email protected]
+casanueva	Olivia	Casanueva	The Babraham Institute	[email protected]
+Wakelam	Michael	Wakelam	The Babraham Institute	[email protected]
+ckaleta	Christoph	Kaleta	Institute for Experimental Medicine, Kiel University	[email protected]
+Weeghel	Michel	van Weeghel	University of Amsterdam	[email protected]
+Safak	Safak L	Yilmaz	University of Massachusetts Medical School	[email protected]
+ms	Manusnan	Suriyalaksh	The Babraham Institute	[email protected]
+Artur	Artur	Bastos Lourenc	Pablo de Olavide University/CABD	[email protected]
+Andrea	Andrea	Hannibal	Max Planck Institute for Biology and Aging	[email protected]
+jpnh	Jake	Hattwell	The University of Queensland	[email protected]

curation/Definition-SBtab.tsv

@@ -0,0 +1,61 @@
+!!SBtab SbtabVersion='1.0' TableType='Definition' TableName='Allowed_types'
+!ComponentName	!ComponentType	!IsPartOf	!Format	!Description
+ID	Column	Reaction	string	Reaction short name
+Name	Column	Reaction	string	Human readable name of the reaction
+ReactionFormula	Column	Reaction	string	Formal description of the reaction
+IsReversible	Column	Reaction	Boolean	Specify if the reaction should be treated as reversible. YES means the reactions is reversible, FALSE means it is irreversible
+GeneAssociation	Column	Reaction	string	Logic expression describing the influence of genes on the reaction fluxes. Its form should be: (gene1) and/or (gene2). The ID should be value of the the !ID field from the Gene table.
+Group	Column	Reaction	string	Groups in which the reaction belong, for instance pathways (but not limited to). Several groups should be separated by <U+0093>;<U+0094>
+Pathway	Column	Reaction	string	Pathways in which the reaction is involved, separated with <U+0093>;<U+0094>. Will become KEGG PATHWAY identifiers at some point
+Identifiers:kegg.reaction	Column	Reaction	string	Cross-references to KEGG reactions. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:pubmed	Column	Reaction	string	Cross-references to PubMed. Only put the numerical identifier is included, no prefix such as <U+0093>PMID:<U+0094>. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:DOI	Column	Reaction	string	Digital Object Identifiers linking to a source of information. Only the identifier is included, no prefix such as <U+0093>DOI:<U+0094>. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:eco	Column	Reaction	string	Cross-reference to terms from the Evidence Ontology.  Note that the prefix <U+0091>ECO:<U+0092> is part of ECO identifiers.
+Comment	Column	Reaction	string	Any free form comment about the row
+Curator	Column	Reaction	string	The identifier of the Curator. The details are in the Curator table
+ID	Column	Gene	string	Gene short name, to be used for the GeneAssociation in the reaction tables
+Identifiers:WormBase	Column	Gene	string	Gene id in Wormbase. Generally of the form <U+0093>WBGene<U+0094> followed by several digits
+Symbol	Column	Gene	string	Standard gene symbol
+Locus	Column	Gene	string	Alternative gene ID, corresponding to the locus. Generally a letter followed by a few digits, a dot, and a digit.
+Name	Column	Gene	string	Human readable name of the gene. It should be the symbol if it exists, the locus ID otherwise
+GO_process	Column	Gene	string	Cross-references to Gene Ontology biological process branch. Note that the prefix <U+0091>GO:<U+0092> is part of Gene Ontology identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+GO_function	Column	Gene	string	Cross-references to Gene Ontology molecular function branch. Note that the prefix <U+0091>GO:<U+0092> is part of Gene Ontology identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+GO_component	Column	Gene	string	Cross-references to Gene Ontology cell component branch. Note that the prefix <U+0091>GO:<U+0092> is part of Gene Ontology identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:ec-code	Column	Gene	string	Cross-references to the Enzyme Classification.  Several cross-ref should be separated by <U+0093>;<U+0094>
+Comment	Column	Gene	string	Any free form comment about the row
+Curator	Column	Gene	string	The identifier of the Curator. The details are in the Curator table
+ID	Column	Compound	string	Compound short name, to be used in the reaction tables
+Name	Column	Compound	string	Human readable name of the compound. Ideally the ChEBI name.
+Location	Column	Compound	string	Compartment where the compound is located. It should be the value of an ID field of the Compartment table.
+Charge	Column	Compound	integer	Electrical charge of the compound
+Formula	Column	Compound	string	Chemical formula, if possible coming from ChEBI
+Identifiers:chebi	Column	Compound	string	Cross-reference to ChEBI. Note that the prefix <U+0091>CHEBI:<U+0092> is part of ChEBI identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:kegg.compound	Column	Compound	string	Cross-reference to KEGG compound. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:pubmed	Column	Compound	string	Cross-reference to PubMed. Only put the numerical identifier is included, no prefix such as <U+0093>PMID:<U+0094>. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:DOI	Column	Compound	string	Digital Object Identifiers linking to a source of information. Only the identifier is included, no prefix such as <U+0093>DOI:<U+0094>. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:eco	Column	Compound	string	Cross-reference to terms from the Evidence Ontology.  Note that the prefix <U+0091>ECO:<U+0092> is part of ECO identifiers.
+Comment	Column	Compound	string	Any free form comment about the row
+Curator	Column	Compound	string	The identifier of the Curator. The details are in the Curator table
+ID	Column	Compartment	string	Compartment short name, to be used in the compound tables
+Name	Column	Compartment	string	Human readable name of the reaction
+Identifiers:go	Column	Compartment	string	Cross-reference to Gene Ontology, cell component branch. Note that the prefix <U+0091>GO:<U+0092> is part of Gene Ontology identifiers. Several cross-ref should be separated by <U+0093>,<U+0094>
+Comment	Column	Compartment	string	Any free form comment about the row
+ID	Column	Pathway	string	Pathway short name, to be used in the reaction table
+Name	Column	Pathway	string	Human readable name of the pathway
+Kind	Column	Pathway	string	Should always be partonomy
+GO_process	Column	Pathway	string	Cross-references to Gene Ontology biological process branch. Note that the prefix <U+0091>GO:<U+0092> is part of Gene Ontology identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+Identifiers:kegg.pathway	Column	Pathway	string	Cross-reference to KEGG PATHWAY. Several cross-ref should be separated by <U+0093>;<U+0094>
+Comment	Column	Pathway	string	Any free form comment about the row
+Curator	Column	Pathway	string	The identifier of the Curator. The details are in the Curator table
+ID	Column	Compound-class	string	Compound-class short name, to be used in the reaction table
+Name	Column	Compound-class	string	Human readable name of the compound class
+Kind	Column	Compound-class	string	Should always be classification
+Identifiers:chebi	Column	Compound-class	string	Cross-reference to the ChEBI entries corresponding to the compound classes. Note that the prefix <U+0091>CHEBI:<U+0092> is part of ChEBI identifiers. Several cross-ref should be separated by <U+0093>;<U+0094>
+Comment	Column	Compound-class	string	Any free form comment about the row
+Curator	Column	Compound-class	string	The identifier of the Curator. The details are in the Curator table
+ID	Column	Curator	string	A unique string that identifies the curator
+given-name	Column	Curator	string	Given name of the curator, including first and middele names
+family-name	Column	Curator	string	Family name or names of the curator
+organization-name	Column	Curator	string	Affiliation of the curator, Several organizations should be separated by ";"
+email	Column	Curator	string	Email address of the curator. Several addresses should be separated by ";"
+Notes	Column	All	string	The columns named <U+0093>!Notes:something<U+0094> contain non-standard information to be included in the "notes" elements of the SBML file and not in bona fide SBML elements