Materials-Consortia · ml-evs · Jun 10, 2024 · Aug 7, 2023 · Aug 7, 2023 · Aug 7, 2023
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,6 +16,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
     - name: Set up Python 3.8
       uses: actions/setup-python@v1
       with:
@@ -31,6 +33,8 @@ jobs:
     timeout-minutes: 5
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:
@@ -43,6 +47,8 @@ jobs:
     timeout-minutes: 5
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
     - run: make audit_authors
 
   audit-spelling:
@@ -51,12 +57,6 @@ jobs:
     timeout-minutes: 5
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
     - run: make audit_spelling
-
-  audit-schemas:
-    name: Audit OpenAPI schemas with swagger validator
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-    - uses: actions/checkout@v2
-    - run: make audit_schemas
diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -0,0 +1,56 @@
+name: Build GitHub pages
+
+on:
+  push:
+    branches:
+      - develop
+  workflow_dispatch:
+
+jobs:
+
+  build_html:
+    runs-on: ubuntu-latest
+
+    env:
+      COMMIT_AUTHOR: OPTIMADE developers
+      COMMIT_AUTHOR_EMAIL: [email protected]
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: pip install docutils
+
+    - name: Run rst2html
+      run: make html
+
+    - name: Configure git
+      run: |
+        git config --global user.name "${COMMIT_AUTHOR}"
+        git config --global user.email "${COMMIT_AUTHOR_EMAIL}"
+
+    - name: Commit to gh-pages
+      run: |
+        git fetch origin gh-pages
+        git checkout gh-pages
+        mkdir -p specification/develop
+        # patch dev specification to include banner
+        sed -i 's|<body class="with-toc">|<body class="with-toc"><div class="banner-container"><div class="banner">This is a development version of the specification.</div></div>|g' optimade.html
+        mv optimade.html specification/develop/index.html
+        git add specification/develop/index.html
+        git commit -m "Deploy develop specification to GitHub Pages: ${SHA}"
+        if git diff --cached --quiet; then
+            exit 0
+        fi
+
+    - name: Push changes
+      uses: ad-m/[email protected]
+      with:
+        branch: gh-pages
+        force: true
+        github_token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,7 @@ Makeconf*
 .idea/
 .vscode/
 .DS_Store
+schemas/output
+schemas/example/output
+*.pdf
+*.html
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "dependencies/submodules/optimade-property-tools"]
+	path = dependencies/submodules/optimade-property-tools
+	url = https://github.com/Materials-Consortia/optimade-property-tools.git
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,9 @@ repos:
       (?x)^(
         tests/inputs/various-whitespace.filter|
         tests/inputs/fuzzystring-leading-trailing-spaces.filter|
-        units/definitions.units
+        external/GNU_Units/definitions.units|
+        units/definitions.units|
+        .words.lst
       )$
 
 - repo: https://github.com/Lucas-C/pre-commit-hooks
@@ -16,3 +18,9 @@ repos:
   - id: remove-tabs
     args: [ '--whitespaces-count', '2']
     files: \.rst$
+
+- repo: https://github.com/rstcheck/rstcheck
+  rev: v6.2.0
+  hooks:
+  - id: rstcheck
+    args: [ '--config', '.rstcheck.cfg' ]
diff --git a/.rstcheck.cfg b/.rstcheck.cfg
@@ -0,0 +1,9 @@
+[rstcheck]
+report_level=WARNING
+ignore_roles=
+    src,
+    RFC,
+    filter
+ignore_languages=
+    filter,
+    python
diff --git a/.words.lst b/.words.lst
@@ -1,69 +1,75 @@
-personal_ws-1.1 en 205
+personal_ws-1.1 en 216 
 ABNF
 ACM
 Aa
 Acta
-Ao
 BaCa
 BadLuck
 Bb
 BibTeX
 CCaO
 CECAM
+CIF
 CSV
 CaCO
 ClNa
 ClosingBrace
 CommonMark
 ConstantFirstComparison
-Cryst
+Cracknell
+Crystallographica
+DOI
+Dordrecht
+EBNF
 EREs
 Edsger
 EqualityOperator
 EscapedChar
 ExpressionClause
 ExpressionPhrase
 FuzzyStringOpRhs
-Grammatica
+Hermann
 IANA
-IEEE
+ITC
+IUCr
 IUPAC's
-IdentifierFirstComparison
-IdentifierZipAddon
+Kluwer
 KnownOpRhs
+LD
 Lausanne
-LengthComparison
 LengthOpRhs
 LowercaseLetter
+Mauguin
 NaCl
-NaN
 NaO
+Namespace
+OPTIMADE
 OpenAPI
 OpeningBrace
-OperatorComparison
 OrderedConstant
 OrderedValue
 POSCAR
 POSIX
-PredicateComparison
 PropertyFirstComparison
 PropertyZipAddon
 Punctuator
+Queryable
+REs
 RST
 RelativeComparisonOperator
 SPDX
-Schmit
 SetOpRhs
 SetZipOpRhs
+Shmueli
 SiGe
 SiO
+Springer
+Substring
+Theo
 URI
-UTC
-UUID
 UnescapedChar
 UnicodeHighChar
 UnorderedConstant
-Unversioned
 UppercaseLetter
 ValueEqRhs
 ValueList
@@ -82,73 +88,74 @@ api
 atime
 backend
 backends
-bandgap
 bd
 booktitle
 boolean
+bzip
 calc
 cartesian
 checksums
 cif
-conformant
+coreCIF
 cr
 crossref
-css
 csv
 ctime
 deNOx
 dec
 denox
 dep
 dependentRequired
+describedby
+designator
 dimensionality
 discoverability
 discoverable
 doi
-downloadable
 eb
 ebnf
 edf
 enum
 exclusiveMaximum
 exclusiveMinimum
 exmpl
+ferroelectric
+fjeiwoj
 fieldname
 firstname
+hdf
+hermann
 howpublished
 href
-html
 http
 hydrogens
 hydroperoxide
 implementers
+incrementing
 internaldb
 javascript
 json
 jsonapi
 jsonc
+jsonlines
 kvak
 lastname
-libc
 lst
-lt
 maintainer's
+mauguin
 maxItems
 maxLength
 maxProperties
 md
-metadata
 minItems
 minLength
 minProperties
-mistyped
 mtime
-multi
 multipleOf
 namespace
 namespaces
 nattached
-nbsp
+nd
 nelements
 nl
 nonperiodic
@@ -158,49 +165,58 @@ occupancies
 ok
 optimade
 organisation
+overbar
+overbars
 oxygens
 param
 pcre
 perovskites
+piezoelectic
 pre
 prepended
 prepending
+prescreen
 prev
 qudt
 queryable
 rc
-regex
 renormalize
 sectnum
 sha
 sortable
 spacegroup
 structs
+subfield
 subfields
 substring
 substrings
 supercell
+symop
+symops
 testdb
-timestamp
-timestamps
+th
+typesetted
 ucum
+undelying
 uniqueItems
 unrequested
 unversioned
 uri
 uris
 url
-urls
 uuid
 vMAJOR
-versioning
 vnd
 vt
 whitespace
-workflow
 xml
 xy
+xyz
 yacc
+yb
 zeo
 zeolites
-ångström
+Ã¥ngstrÃ¶m
+ÃƒÂ¥ngstrÃƒÂ¶m
+ÃƒÆ’Ã‚Â¥ngstrÃƒÆ’Ã‚Â¶m
+incrementing