Merge pull request #1402 from nextstrain/chore/cleanup

.env.example

@@ -1,12 +1,16 @@
+# URL to `osxcross.tar.xz` file containing osxcross toolchain
+# distribution (https://github.com/tpoechtrager/osxcross) used for cross-compilation
+# from Linux to macOS. See `tools/osxcross/README.md` for instructions on how to
+# produce it. Refer to osxcross documentation for more info.
+# This is only needed if you are on Linux and want to produce binaries for macOS.
 OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz
 
 FULL_DOMAIN=autodetect
 
 WEB_PORT_DEV=3000
 WEB_PORT_PROD=8080
-WEB_PORT_ANALYZE=8888
 
-DATA_LOCAL_PORT=27722
+DATA_LOCAL_PORT=3001
 
 NEXT_TELEMETRY_DISABLED=1
 RECOIL_DUPLICATE_ATOM_KEY_CHECKING_ENABLED=false
@@ -23,47 +27,11 @@ PROD_ENABLE_STYLELINT=1
 ANALYZE=0
 PROFILE=0
 
-# Destination for `rsync` command when using `make sync`.
-# Any destination, local or remote, is accepted.
-SYNC_DESTINATION=123.456.789.123:~/nextclade
-
 # URL of Nextclade datasets server. See: https://github.com/neherlab/nextclade_data
-# Replace this with `http://localhost:27722` to use local data server instead
+# Replace this with `http://localhost:3001` to use local data server instead
 DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3
-# DATA_FULL_DOMAIN=http://localhost:27722
+# DATA_FULL_DOMAIN=http://localhost:3001
 
 # If enabled, Nextclade Web will first attempt to fetch datasets from the corresponding GitHub branch. If this attempt
 # fails, it will use `DATA_FULL_DOMAIN` as usual.
 DATA_TRY_GITHUB_BRANCH=0
-
-# Directory path (relative to the root of the project) from which local data server takes the data.
-# Useful for local testing on new datasets. See: https://github.com/neherlab/nextclade_data
-# It is recommended to keep the `nextclade_data` git repo in a sibling directory of `nextclade` git repo.
-DATA_OUTPUT_DIR_RELATIVE=../nextclade_data/data_output
-
-master_AWS_ACCESS_KEY_ID=
-master_AWS_SECRET_ACCESS_KEY=
-master_AWS_CLOUDFRONT_DISTRIBUTION_ID=
-master_AWS_S3_BUCKET=nextclade-master
-master_ENV_NAME=master
-master_FULL_DOMAIN=https://master.clades.nextstrain.org
-master_DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org
-master_AWS_DEFAULT_REGION=us-east-1
-
-staging_AWS_ACCESS_KEY_ID=
-staging_AWS_SECRET_ACCESS_KEY=
-staging_AWS_CLOUDFRONT_DISTRIBUTION_ID=
-staging_AWS_S3_BUCKET=nextclade-staging
-staging_ENV_NAME=staging
-staging_FULL_DOMAIN=https://staging.clades.nextstrain.org
-staging_DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org
-staging_AWS_DEFAULT_REGION=us-east-1
-
-release_AWS_ACCESS_KEY_ID=
-release_AWS_SECRET_ACCESS_KEY=
-release_AWS_CLOUDFRONT_DISTRIBUTION_ID=
-release_AWS_S3_BUCKET=nextclade-release
-release_ENV_NAME=release
-release_FULL_DOMAIN=https://clades.nextstrain.org
-release_DATA_FULL_DOMAIN=https://data.clades.nextstrain.org
-release_AWS_DEFAULT_REGION=us-east-1

.github/workflows/builder-docker-image.yml

@@ -58,4 +58,4 @@ jobs:
         run: |
           cp .env.example .env
           sed -i -e "s|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}|g" .env
-          ./docker-dev docker-image-build-push
+          ./docker/dev docker-image-build-push

.github/workflows/cli.yml

@@ -129,11 +129,11 @@ jobs:
 
       - name: "Build docker image (${{ matrix.arch }})"
         run: |
-          CROSS="${{ matrix.arch }}" ./docker-dev docker-image-build-push
+          CROSS="${{ matrix.arch }}" ./docker/dev docker-image-build-push
 
       - name: "Build CLI (${{ matrix.arch }})"
         run: |
-          CROSS="${{ matrix.arch }}" ./docker-dev build-release
+          CROSS="${{ matrix.arch }}" ./docker/dev build-release
 
       - name: "Upload build artifacts (${{ matrix.arch }})"
         uses: actions/upload-artifact@v4
@@ -185,7 +185,7 @@ jobs:
 
       - name: "Run unit tests"
         run: |
-          ./docker-dev test
+          ./docker/dev test
 
 
   run-lints:
@@ -231,7 +231,7 @@ jobs:
 
       - name: "Run lints"
         run: |
-          ./docker-dev lint-ci
+          ./docker/dev lint-ci
 
 
   run-smoke-tests:

.github/workflows/web.yml

@@ -118,27 +118,27 @@ jobs:
 
       - name: "Build docker image"
         run: |
-          CROSS="wasm32-unknown-unknown" ./docker-dev docker-image-build-push
+          CROSS="wasm32-unknown-unknown" ./docker/dev docker-image-build-push
 
       - name: "Install Node.js packages"
         run: |
-          ./docker-dev web yarn install
+          ./docker/dev web yarn install
 
       - name: "Build WebAssembly module"
         run: |
-          ./docker-dev wasm-release
+          ./docker/dev wasm-release
 
       - name: "Build web app"
         run: |
-          ./docker-dev web-release
+          ./docker/dev web-release
 
       - name: "Lint web app code"
         run: |
-          ./docker-dev web yarn lint:ci
+          ./docker/dev web yarn lint:ci
 
       - name: "Lint Rust code"
         run: |
-          ./docker-dev lint-ci
+          ./docker/dev lint-ci
 
       - name: "Upload build artifacts"
         uses: actions/upload-artifact@v4

.gitignore

@@ -30,7 +30,6 @@
 \.tmp
 \.Trashes
 \.vscode/*
-!.vscode/settings.json
 ehthumbs.db
 node_modules/
 Thumbs.db