Merge pull request #83 from microbiomedata/77-finalize-website-struct…

…ure-for-initial-review

Display banners, customize favicon, implement "Edit on GitHub" links, and move some files

.docker/README.md

@@ -0,0 +1,3 @@
+# `.docker`
+
+This directory contains files that are specific to the container-based development environment of this repository.

.docker/dev.nginx.conf

@@ -0,0 +1,46 @@
+# This is an Nginx configuration file used for previewing the website locally.
+# It maps top-level paths to the containers that serve the associated resources.
+# The hostnames here match the service names defined in `docker-compose.yml`.
+
+events {}
+
+http {
+    server {
+        listen 80;
+
+        # Legacy documentation.
+        location /legacy/ {
+            proxy_pass http://legacy-nmdc-documentation:8000/;
+        }
+
+        # Redirect `/legacy` (exact) to `/legacy/`.
+        location = /legacy {
+            rewrite ^ $scheme://$http_host/legacy/ redirect;
+        }
+
+        # Runtime documentation.
+        location /runtime/ {
+            proxy_pass http://runtime-documentation:8000/;
+        }
+
+        # Redirect `/runtime` (exact) to `/runtime/`.
+        location = /runtime {
+            rewrite ^ $scheme://$http_host/runtime/ redirect;
+        }
+
+        # Workflow documentation.
+        location /workflows/ {
+            proxy_pass http://workflow-documentation:8000/;
+        }
+
+        # Redirect `/workflows` (exact) to `/workflows/`.
+        location = /workflows {
+            rewrite ^ $scheme://$http_host/workflows/ redirect;
+        }
+
+        # Current NMDC documentation.
+        location / {
+            proxy_pass http://nmdc-documentation:8000/;
+        }
+    }
+}

.github/workflows/fetch-and-compile-workflow-documentation.yml

@@ -27,14 +27,14 @@ jobs:
         #
       - name: Fetch documentation sources and arrange into chapters
         run: |
-          chmod +x ./src/workflow_docs/fetch_docs_sources.sh
-          ./src/workflow_docs/fetch_docs_sources.sh
+          chmod +x ./src/ingesters/workflow_docs/fetch_docs_sources.sh
+          ./src/ingesters/workflow_docs/fetch_docs_sources.sh
       - name: Introduce additional source documents and a configuration file
         run: |
-          cp -r src/workflow_docs/metagenome_workflow_overview/docs /tmp/book/src/chapters/1_Metagenome_Workflow_Overview
-          cp    src/workflow_docs/overview.rst                      /tmp/book/src/chapters/overview.rst
-          cp    src/workflow_docs/index.rst                         /tmp/book/src/index.rst
-          cp    src/workflow_docs/conf.py                           /tmp/book/src/conf.py
+          cp -r src/ingesters/workflow_docs/metagenome_workflow_overview/docs /tmp/book/src/chapters/1_Metagenome_Workflow_Overview
+          cp    src/ingesters/workflow_docs/overview.rst                      /tmp/book/src/chapters/overview.rst
+          cp    src/ingesters/workflow_docs/index.rst                         /tmp/book/src/index.rst
+          cp    src/ingesters/workflow_docs/conf.py                           /tmp/book/src/conf.py
       - name: Compile source documents into HTML
         run: sphinx-build --builder html /tmp/book/src ${{ github.workspace }}/_dist
         # Upload the result as an "artifact" so it can then be downloaded and used by another job.

README.md

@@ -221,7 +221,7 @@ docker compose up --detach      workflow-documentation
 ```
 
 If you **only** make changes to the documentation source files that reside in _this_ repository
-(i.e. those in `src/workflow_docs`), then you can issue this sequence of commands instead,
+(i.e. those in `src/ingesters/workflow_docs`), then you can issue this sequence of commands instead,
 which will allow Docker to _avoid refetching_ the source files from the upstream repos:
 
 ```shell