Merge remote-tracking branch 'origin/master' into docs/v3

nextstrain · Oct 11, 2023 · 61abb19 · 61abb19
2 parents cd9a8c6 + 5fbe04c
commit 61abb19
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diff --git a/.env.example b/.env.example
@@ -29,9 +29,13 @@ 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
-DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org
+DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3
 # DATA_FULL_DOMAIN=http://localhost:27722
 
+# 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.

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,2 +1 @@
-vers
 blank_issues_enabled: false
diff --git a/.github/workflows/cli.yml b/.github/workflows/cli.yml
@@ -57,17 +57,17 @@ jobs:
       - name: "Setup environment (release)"
         if: endsWith(github.ref, '/release-cli')
         run: |
-          echo "DATA_FULL_DOMAIN=https://data.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.clades.nextstrain.org/v3" >> $GITHUB_ENV
 
       - name: "Setup environment (staging)"
         if: endsWith(github.ref, '/staging-cli')
         run: |
-          echo "DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org/v3" >> $GITHUB_ENV
 
       - name: "Setup environment (master)"
         if: ${{ !endsWith(github.ref, '/staging-cli') && !endsWith(github.ref, '/release-cli') }}
         run: |
-          echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3" >> $GITHUB_ENV
 
       - name: "Checkout code"
         uses: actions/checkout@v3
@@ -106,7 +106,7 @@ jobs:
         run: |
           cp .env.example .env
           sed -i -e "s|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}|g" .env
-          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}|g" .env
+          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}|g" .env
 
       - name: "Login to Docker Hub"
         uses: docker/login-action@v2
@@ -170,7 +170,6 @@ 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
-          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|g" .env
 
       - name: "Run unit tests"
         run: |
@@ -217,7 +216,6 @@ 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
-          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|g" .env
 
       - name: "Run lints"
         run: |

diff --git a/.github/workflows/web.yml b/.github/workflows/web.yml
@@ -37,23 +37,23 @@ jobs:
         run: |
           echo "ENV_NAME=release" >> $GITHUB_ENV
           echo "FULL_DOMAIN=https://clades.nextstrain.org" >> $GITHUB_ENV
-          echo "DATA_FULL_DOMAIN=https://data.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.clades.nextstrain.org/v3" >> $GITHUB_ENV
           echo "PLAUSIBLE_IO_DOMAIN=clades.nextstrain.org" >> $GITHUB_ENV
 
       - name: "Setup environment (staging)"
         if: endsWith(github.ref, '/staging')
         run: |
           echo "ENV_NAME=staging" >> $GITHUB_ENV
           echo "FULL_DOMAIN=https://staging.clades.nextstrain.org" >> $GITHUB_ENV
-          echo "DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.staging.clades.nextstrain.org/v3" >> $GITHUB_ENV
           echo "PLAUSIBLE_IO_DOMAIN=staging.clades.nextstrain.org" >> $GITHUB_ENV
 
       - name: "Setup environment (master)"
         if: ${{ !endsWith(github.ref, '/staging') && !endsWith(github.ref, '/release') }}
         run: |
           echo "ENV_NAME=master" >> $GITHUB_ENV
           echo "FULL_DOMAIN=https://master.clades.nextstrain.org" >> $GITHUB_ENV
-          echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org" >> $GITHUB_ENV
+          echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3" >> $GITHUB_ENV
           echo "PLAUSIBLE_IO_DOMAIN=master.clades.nextstrain.org" >> $GITHUB_ENV
 
       - name: "Checkout code"
@@ -107,7 +107,7 @@ jobs:
         run: |
           cp .env.example .env
           sed -i -e "s|FULL_DOMAIN=autodetect|FULL_DOMAIN=${FULL_DOMAIN}|g" .env
-          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}|g" .env
+          sed -i -e "s|DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org/v3|DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}|g" .env
 
       - name: "Login to Docker Hub"
         uses: docker/login-action@v2

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,6 +1,11 @@
 ---
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
 conda:
   environment: docs/environment.yml
 

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/docker-dev b/docker-dev
@@ -545,10 +545,8 @@ ${NICE} docker run --rm \
 if [ -n "${CROSS:-}" ] && [ -n "${RELEASE:-}" ] && { [ "${BUILD:-}" == 1 ] || [ "${RUN:-}" == 1 ]; }; then
   mkdir -p .out/
   if [[ "${CROSS}" == *windows* ]]; then
-    cp "${BUILD_DIR}/${CROSS}/release/nextalign.exe" ".out/nextalign-${CROSS}.exe"
     cp "${BUILD_DIR}/${CROSS}/release/nextclade.exe" ".out/nextclade-${CROSS}.exe"
   else
-    cp "${BUILD_DIR}/${CROSS}/release/nextalign" ".out/nextalign-${CROSS}"
     cp "${BUILD_DIR}/${CROSS}/release/nextclade" ".out/nextclade-${CROSS}"
   fi
 fi
diff --git a/docker/docker-prod-alpine.dockerfile b/docker/docker-prod-alpine.dockerfile
@@ -1,8 +1,8 @@
 FROM alpine:3
 
 COPY .out/nextclade-x86_64-unknown-linux-musl /usr/bin/nextclade
-COPY .out/nextalign-x86_64-unknown-linux-musl /usr/bin/nextalign
 
 RUN set -eux \
+&& ln -s /usr/bin/nextclade /usr/bin/nextalign \
 && ln -s /usr/bin/nextclade /nextclade \
 && ln -s /usr/bin/nextalign /nextalign
diff --git a/docker/docker-prod-debian.dockerfile b/docker/docker-prod-debian.dockerfile
@@ -1,9 +1,9 @@
 FROM debian:11
 
 COPY .out/nextclade-x86_64-unknown-linux-gnu /usr/bin/nextclade
-COPY .out/nextalign-x86_64-unknown-linux-gnu /usr/bin/nextalign
 
 RUN set -eux \
+&& ln -s /usr/bin/nextclade /usr/bin/nextalign \
 && ln -s /usr/bin/nextclade /nextclade \
 && ln -s /usr/bin/nextalign /nextalign \
 && export DEBIAN_FRONTEND=noninteractive \

diff --git a/docker/docker-prod-scratch.dockerfile b/docker/docker-prod-scratch.dockerfile
@@ -1,4 +1,6 @@
 FROM scratch
 
 COPY .out/nextclade-x86_64-unknown-linux-musl /nextclade
-COPY .out/nextalign-x86_64-unknown-linux-musl /nextalign
+
+RUN set -eux \
+&& ln -s /usr/bin/nextclade /usr/bin/nextalign