Refactor CI. (#41)

* Refactor CI.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* add shell: bash

* Reusable workflows?

* Simplify?

* Rename steps?

* Old names but without needs

* Descriptions trip it up.

* Refactor push-main too

* Nicer names of two main workflows

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/deploy.yml → .github/workflows/build-docs.yml

@@ -1,13 +1,10 @@
 ---
-name: CI docs
-
+name: Build docs
 on:
-    push:
-        branches:
-            - main
+    workflow_call:
 
 jobs:
-    build-pages:
+    build-docs:
         runs-on: windows-latest
         steps:
             - uses: actions/checkout@v3
@@ -23,25 +20,40 @@ jobs:
                       requirements*.txt
 
             - name: Install dependencies
+              shell: bash
               run: |
                   python -m pip install --upgrade pip
                   pip install -r requirements.txt
                   pip install -r requirements-docs.txt
+
+            - name: Check environment
+              shell: bash
+              run: |
                   pip freeze
 
             - name: Build base docs
+              shell: bash
               run: |
                   gen-doc schemas/base.yaml -d docs/source/gen-doc --template-directory docs/source/_templates
 
             - name: Build FileType docs
+              shell: bash
               run: |
                   gen-doc schemas/filetype.yml -d docs/source/gen-doc --template-directory docs/source/_templates
 
             - name: Build Extractor docs
+              shell: bash
               run: |
                   gen-doc schemas/extractor.yml -d docs/source/gen-doc --template-directory docs/source/_templates
 
+            - name: Upload gen-doc artifact
+              uses: actions/upload-artifact@v3
+              with:
+                  name: gen-doc
+                  path: docs/source/gen-doc
+
             - name: Build Sphinx docs
+              shell: bash
               run: |
                   sphinx-build -b html docs/source public/main
 
@@ -50,24 +62,3 @@ jobs:
               with:
                   name: public-main
                   path: public/main
-    deploy-pages:
-        runs-on: ubuntu-latest
-        needs:
-            - build-pages
-        steps:
-            - uses: actions/checkout@v3
-
-            - uses: actions/setup-python@v4
-              with:
-                  python-version: '3.10'
-
-            - uses: actions/download-artifact@v3
-              with:
-                  name: public-main
-                  path: public/main
-
-            - uses: peaceiris/actions-gh-pages@v3
-              with:
-                  github_token: ${{ secrets.GITHUB_TOKEN }}
-                  publish_dir: ./public
-                  keep_files: true

.github/workflows/check-linkml-schemas.yml

@@ -0,0 +1,51 @@
+---
+name: Check LinkML schemas
+on:
+    workflow_call:
+
+jobs:
+    check-linkml-schemas:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v3
+              with:
+                  submodules: true
+
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: '3.10'
+                  cache: pip
+                  cache-dependency-path: |
+                      requirements*.txt
+
+            - name: Install dependencies
+              shell: bash
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install -U setuptools wheel
+                  pip install -r requirements.txt
+
+            - name: Check environment
+              shell: bash
+              run: |
+                  pip freeze
+
+            - name: Run LinkML generators
+              shell: bash
+              run: |
+                  for f in $(ls schemas/*); do
+                    gen-pydantic -vvv --stacktrace $f
+                    gen-json-schema -vvv --stacktrace $f
+                  done
+
+            - name: Validate examples
+              shell: bash
+              run: |
+                  for f in $(ls examples/extractor/*.yml); do
+                    linkml-validate -s schemas/extractor.yml -C Extractor $f
+                  done
+
+                  for f in $(ls examples/filetype/*.yml); do
+                    linkml-validate -s schemas/filetype.yml -C FileType $f
+                  done

.github/workflows/pull-request.yml

@@ -0,0 +1,22 @@
+---
+name: CI PR
+
+on:
+    pull_request:
+        branches:
+            - main
+
+# Cancel running workflows when additional changes are pushed
+# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
+concurrency:
+    group: ${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
+
+jobs:
+
+    call-check-linkml-schemas:
+        uses: ./.github/workflows/check-linkml-schemas.yml
+
+    call-build-docs:
+        needs: [call-check-linkml-schemas]
+        uses: ./.github/workflows/build-docs.yml

.github/workflows/push-main.yml

@@ -0,0 +1,39 @@
+---
+name: CI main
+
+on:
+    push:
+        branches:
+            - main
+
+
+jobs:
+
+    call-check-linkml-schemas:
+        uses: ./.github/workflows/check-linkml-schemas.yml
+
+    call-build-docs:
+        needs: [call-check-linkml-schemas]
+        uses: ./.github/workflows/build-docs.yml
+
+    deploy-pages:
+        runs-on: ubuntu-latest
+        needs: [call-build-docs]
+        steps:
+            - uses: actions/checkout@v3
+
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: '3.10'
+
+            - uses: actions/download-artifact@v3
+              with:
+                  name: public-main
+                  path: public/main
+
+            - uses: peaceiris/actions-gh-pages@v3
+              with:
+                  github_token: ${{ secrets.GITHUB_TOKEN }}
+                  publish_dir: ./public
+                  keep_files: true