Set up continuous integration

.github/workflows/check.yml

@@ -0,0 +1,31 @@
+name: continuous integration
+on: [push, pull_request]
+permissions:
+  contents: read
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Go 1.22
+        uses: actions/setup-go@v5
+        with:
+          go-version: "1.22.x"
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: install Pipenv
+        run: pip install pipenv --user
+      - name: install dependencies
+        run: pipenv sync --dev # Installs all deps, including dev deps, from Pipfile.lock.
+      - name: Create .env file for GitHub Actions
+        run: pipenv run invoke mkenv
+      - name: format
+        run: pipenv run invoke fmt
+      - name: lint
+        run: pipenv run invoke lint
+      - name: check types
+        run: pipenv run invoke build
+      - name: run tests
+        run: pipenv run invoke test

LICENSE.md

@@ -15,4 +15,4 @@ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PA
 PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT
 OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
+OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,4 +1,6 @@
 # Human Leukocyte Antigen (HLA) Curation Interface
 
+[![CI](https://github.com/clingen/stanford-hci/actions/workflows/check.yml/badge.svg)](https://github.com/clingen/stanford-hci/actions)
+
 The HCI is under development. See our [roadmap](https://github.com/ClinGen/stanford-hci/issues/1)
-and our [docs](./doc).
+and our [docs](./doc).

doc/README.md

@@ -1,26 +1,26 @@
 # Documentation
 
 - [Tutorials](./tutorial.md) (learning-oriented)
-    - Tutorials are lessons that take the reader by the hand through a series of
-      steps to complete a project of some kind. Unlike how-to guides, tutorials
-      don't assume lots of prerequisite knowledge.
+  - Tutorials are lessons that take the reader by the hand through a series of
+    steps to complete a project of some kind. Unlike how-to guides, tutorials
+    don't assume lots of prerequisite knowledge.
 - [How-to guides](./howto.md) (problem-oriented)
-    - How-to guides take the reader through the steps required to solve a
-      real-world problem. They are recipes, directions to achieve a specific end.
-      Unlike tutorials, they typically assume a fair amount of prerequisite
-      knowledge.
+  - How-to guides take the reader through the steps required to solve a
+    real-world problem. They are recipes, directions to achieve a specific end.
+    Unlike tutorials, they typically assume a fair amount of prerequisite
+    knowledge.
 - [Explanations](./explanation.md) (understanding-oriented)
-    - Explanation, or discussions, clarify and illuminate a particular topic. They
-      broaden the documentation’s coverage of a topic. Explanations can equally
-      well be described as discussions; they are discursive in nature. They are a
-      chance for the documentation to relax and step back from the software,
-      taking a wider view, illuminating it from a higher level or even from
-      different perspectives. You might imagine a discussion document being read
-      at leisure, rather than over the code.
+  - Explanation, or discussions, clarify and illuminate a particular topic. They
+    broaden the documentation’s coverage of a topic. Explanations can equally
+    well be described as discussions; they are discursive in nature. They are a
+    chance for the documentation to relax and step back from the software,
+    taking a wider view, illuminating it from a higher level or even from
+    different perspectives. You might imagine a discussion document being read
+    at leisure, rather than over the code.
 - Reference guides (information-oriented)
-    - Reference guides are technical descriptions of the machinery and how to
-      operate it. Reference guides have one job only: to describe. They are
-      code-determined, because ultimately that’s what they describe: key classes,
-      functions, APIs, and so they should list things like functions, fields,
-      attributes and methods, and set out how to use them. For this project,
-      reference is code comments (Go doc comments).
+  - Reference guides are technical descriptions of the machinery and how to
+    operate it. Reference guides have one job only: to describe. They are
+    code-determined, because ultimately that’s what they describe: key classes,
+    functions, APIs, and so they should list things like functions, fields,
+    attributes and methods, and set out how to use them. For this project,
+    reference is code comments (Go doc comments).

doc/explanation.md

@@ -1 +1 @@
-# Explanations
+# Explanations

doc/howto.md

@@ -1 +1 @@
-# How-to guides
+# How-to guides

doc/tutorial.md

@@ -1 +1 @@
-# Tutorials
+# Tutorials

tasks.py

@@ -3,10 +3,12 @@
 All command line tasks should be defined in this file. The only
 exception to this is managing dependencies.
 
-All commands in this file assume you're in the root directory and
+All commands in this file assume you're in the root directory, and
 you've activated the virtual environment.
 """
 
+import os
+
 # Invoke always requires a context parameter, even if it ends up going
 # unused. As of this writing, there are a handful of tasks that don't
 # use their context parameters.
@@ -27,16 +29,15 @@
 TEMPLATE_CONF = dotenv_values(ENV_TEMPLATE)
 ACTUAL_CONF = dotenv_values(ENV_ACTUAL)
 
-# Absolute paths to src and build directories:
-SRC_DIR = f"{ACTUAL_CONF['HCI_ROOT_DIR']}/src"
-BUILD_DIR = f"{ACTUAL_CONF['HCI_ROOT_DIR']}/build"
-
 
 @task
 def fmt(c):
     """Format code."""
     c.run("go fmt ./...")
     c.run("black tasks.py")
+    if not os.getenv("GITHUB_ACTIONS"):
+        c.run("yamlfmt ./.github/**/*")
+    c.run("mdformat .")
 
 
 @task
@@ -49,13 +50,13 @@ def lint(c):
 @task
 def clean(c):
     """Remove old binary."""
-    c.run(f"rm -rf {BUILD_DIR}/*")
+    c.run("rm -rf build/*")
 
 
 @task
 def build(c):
     """Build the binary."""
-    c.run(f"go build -o {BUILD_DIR}/hci {SRC_DIR}")
+    c.run("go build -o build/hci ./src")
 
 
 @task
@@ -86,4 +87,13 @@ def check(c):
 @task
 def dev(c):
     """Run the development server."""
-    c.run(f"source {ENV_ACTUAL} && go run {SRC_DIR}/main.go")
+    c.run(f"source {ENV_ACTUAL} && go run src/main.go")
+
+
+@task
+def mkenv(c):
+    """Make a .env file for GitHub Actions."""
+    c.run("touch ${GITHUB_WORKSPACE}/.env")
+    c.run(
+        "echo \"export HCI_ROOT_DIR='$GITHUB_WORKSPACE'\" >> ${GITHUB_WORKSPACE}/.env"
+    )