Merge pull request #892 from tsalo/schema-package

[SCHEMA] Reorganize schema code into a package

.circleci/config.yml

@@ -11,6 +11,7 @@ jobs:
           command: |
             python -m pip install --upgrade pip
             pip install -r requirements.txt
+            pip install ~/project/tools/schemacode/
       - run:
           name: generate docs
           command: mkdocs build --clean --strict --verbose

.gitattributes

@@ -2,3 +2,4 @@
 *.png -text
 *.jpg -text
 *.webm -text
+tools/schemacode/schemacode/_version.py export-subst

.github/workflows/schemacode_ci.yml

@@ -0,0 +1,94 @@
+name: "schemacode_ci"
+
+on:
+  push:
+    branches:
+      - "master"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
+  pull_request:
+    branches:
+      - "*"
+    paths:
+      - "tools/schemacode/**"
+      - "src/schema/**"
+
+jobs:
+  check_skip:
+    runs-on: ubuntu-latest
+    outputs:
+      skip: ${{ steps.result_step.outputs.ci-skip }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - id: result_step
+        uses: mstachniuk/ci-skip@master
+        with:
+          commit-filter: "[skip ci];[ci skip];[skip github]"
+          commit-filter-separator: ";"
+
+  run_tests:
+    needs: check_skip
+    if: ${{ needs.check_skip.outputs.skip == 'false' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest"]
+            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v2
+        with:
+            python-version: ${{ matrix.python-version }}
+
+      - name: "Display Python version"
+        shell: bash {0}
+        run: python -c "import sys; print(sys.version)"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[tests]
+
+      - name: "Run tests"
+        shell: bash {0}
+        run: |
+          python -m pytest --pyargs schemacode --cov=schemacode ./tools/schemacode/
+
+      - name: "Upload coverage to CodeCov"
+        uses: codecov/codecov-action@v1
+        if: success()
+
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint schemacode
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.7"
+
+      - name: "Install the schemacode package"
+        shell: bash {0}
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools wheel
+          python -m pip install -e ./tools/schemacode[tests]
+
+      - name: "Run flake8"
+        working-directory: ./tools/schemacode/
+        shell: bash {0}
+        run: |
+          flake8 .

CODEOWNERS

@@ -18,3 +18,7 @@
 /src/05-derivatives/05-functional-derivatives.md @effigies
 /src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 /src/99-appendices/06-meg-file-formats.md @monkeyman192
+
+# The schema
+/src/schema/ @tsalo
+/tools/schemacode/ @tsalo

requirements.txt

@@ -4,6 +4,4 @@ pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3
 mkdocs-macros-plugin
 numpy
-pandas
-PYYaml
-tabulate
+tools/schemacode/

tools/mkdocs_macros_bids/macros.py

@@ -2,11 +2,12 @@
 import os
 import sys
 
+from schemacode import render, schema, utils
+
 code_path = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
 sys.path.append(code_path)
 
 from examplecode import example
-from schemacode import schema, utils
 
 
 def make_filename_template(**kwargs):
@@ -28,7 +29,7 @@ def make_filename_template(**kwargs):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    codeblock = schema.make_filename_template(schema_obj, **kwargs)
+    codeblock = render.make_filename_template(schema_obj, **kwargs)
     return codeblock
 
 
@@ -50,7 +51,7 @@ def make_entity_table(**kwargs):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_entity_table(schema_obj, **kwargs)
+    table = render.make_entity_table(schema_obj, **kwargs)
     return table
 
 
@@ -66,7 +67,7 @@ def make_entity_definitions():
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    text = schema.make_entity_definitions(schema_obj)
+    text = render.make_entity_definitions(schema_obj)
     return text
 
 
@@ -81,7 +82,7 @@ def make_glossary():
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    text = schema.make_glossary(schema_obj)
+    text = render.make_glossary(schema_obj)
     return text
 
 
@@ -101,7 +102,7 @@ def make_suffix_table(suffixes):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_suffix_table(schema_obj, suffixes)
+    table = render.make_suffix_table(schema_obj, suffixes)
     return table
 
 
@@ -126,7 +127,7 @@ def make_metadata_table(field_info):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_metadata_table(schema_obj, field_info)
+    table = render.make_metadata_table(schema_obj, field_info)
     return table
 
 
@@ -151,7 +152,7 @@ def make_columns_table(column_info):
     """
     schemapath = utils.get_schema_path()
     schema_obj = schema.load_schema(schemapath)
-    table = schema.make_columns_table(schema_obj, column_info)
+    table = render.make_columns_table(schema_obj, column_info)
     return table
 
 

tools/schemacode/MANIFEST.in

@@ -0,0 +1,2 @@
+include versioneer.py
+include schemacode/_version.py

tools/schemacode/README.md

@@ -0,0 +1,6 @@
+# schemacode
+
+A Python library for working with the BIDS schema.
+
+[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![codecov](https://codecov.io/gh/bids-standard/bids-specification/branch/master/graph/badge.svg)](https://codecov.io/gh/bids-standard/bids-specification)

tools/schemacode/pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+
+[tool.black]
+line-length = 99
+target-version = ['py37']
+include = '\.pyi?$'
+exclude = '''
+(
+  /(
+      \.eggs         # exclude a few common directories in the
+    | \.git          # root of the project
+    | \.github
+    | \.hg
+    | \.pytest_cache
+    | _build
+    | build
+    | dist
+  )/
+  | versioneer.py
+  | schemacode/_version.py
+)
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3

tools/schemacode/schemacode/__init__.py

@@ -0,0 +1,12 @@
+"""A Python package for working with the BIDS schema."""
+from . import render, schema, utils
+
+__all__ = [
+    "render",
+    "schema",
+    "utils",
+]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]