chore: find & replace packages_rs -> packages

Preparation for mv packages_rs packages

.github/dependabot.yml

@@ -12,7 +12,7 @@
 version: 2
 updates:
   - package-ecosystem: "npm"
-    directory: "/packages_rs/nextclade-web/"
+    directory: "/packages/nextclade-web/"
     schedule:
       interval: "daily"
     allow:

.github/workflows/cli.yml

@@ -111,7 +111,7 @@ jobs:
         run: |
           export PATH="${PATH}:${HOME}/bin"
 
-          version=$(dasel select -p toml -s ".package.version" -f "packages_rs/nextclade/Cargo.toml")
+          version=$(dasel select -p toml -s ".package.version" -f "packages/nextclade/Cargo.toml")
           if [[ "$version" =~ (rc|beta|alpha) ]]; then
               export DATA_FULL_DOMAIN="https://data.master.clades.nextstrain.org/v3"
           fi

.github/workflows/web.yml

@@ -83,7 +83,7 @@ jobs:
           path: |
             .build/
             .cache/docker/.cargo
-            packages_rs/nextclade-web/.build/docker
+            packages/nextclade-web/.build/docker
           key: cache-v1-cargo-${{ runner.os }}-wasm32-unknown-unknown-${{ hashFiles('**/Cargo.lock') }}
           restore-keys: |
             cache-v1-cargo-${{ runner.os }}-wasm32-unknown-unknown-${{ hashFiles('**/Cargo.lock') }}
@@ -94,9 +94,9 @@ jobs:
         uses: actions/cache@v4
         with:
           path: |
-            packages_rs/nextclade-web/.build/production/tmp/cache
-            packages_rs/nextclade-web/.cache
-            packages_rs/nextclade-web/node_modules
+            packages/nextclade-web/.build/production/tmp/cache
+            packages/nextclade-web/.cache
+            packages/nextclade-web/node_modules
           key: cache-v1-web-${{ runner.os }}-wasm32-unknown-unknown-${{ hashFiles('**/yarn.lock') }}
           restore-keys: |
             cache-v1-web-${{ runner.os }}-wasm32-unknown-unknown-${{ hashFiles('**/yarn.lock') }}
@@ -144,7 +144,7 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: out
-          path: "packages_rs/nextclade-web/.build/production/web"
+          path: "packages/nextclade-web/.build/production/web"
 
 
   deploy-web:
@@ -191,7 +191,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: "out"
-          path: "packages_rs/nextclade-web/.build/production/web"
+          path: "packages/nextclade-web/.build/production/web"
 
       - name: "Install deploy dependencies"
         run: |
@@ -218,7 +218,7 @@ jobs:
           git config user.email "${{ secrets.GIT_USER_EMAIL }}"
           git config user.name "${{ secrets.GIT_USER_NAME }}"
 
-          pushd packages_rs/nextclade-web  >/dev/null
+          pushd packages/nextclade-web  >/dev/null
 
           export version=$(node -e "\
             const pkg = require('./package.json'); \

.gitignore

@@ -7,8 +7,8 @@
 /e2e/cli/snapshots/
 /e2e/cli/tmp/
 /example-data/
-/packages_rs/*/target/
-/packages_rs/nextclade-web/src/gen
+/packages/*/target/
+/packages/nextclade-web/src/gen
 /paper/paper.pdf
 /paper/preprint.pdf
 /paper/tex2pdf*

Cargo.toml

@@ -1,10 +1,9 @@
 [workspace]
 
 members = [
-  "packages_rs/*",
+  "packages/*",
 ]
 
 exclude = [
-  "packages_rs/3rdparty",
-  "packages_rs/tree-builder-prototype"
+  "packages/3rdparty",
 ]

README.md

@@ -109,7 +109,7 @@ by Nextstrain team
 
   <a href="packages/web/package.json">
     <img
-      src="https://img.shields.io/github/package-json/v/nextstrain/nextclade/master/packages_rs/nextclade-web?label=web&logo=npm"
+      src="https://img.shields.io/github/package-json/v/nextstrain/nextclade/master/packages/nextclade-web?label=web&logo=npm"
       alt="package.json version"
     />
   </a>

docker/dev

@@ -116,10 +116,10 @@ export FILES_TO_WATCH="\
 -w 'Cargo.lock' \
 -w 'Cargo.toml' \
 -w 'clippy.toml' \
--w 'packages_rs/nextclade-web/src' \
--w 'packages_rs/nextclade-web/Cargo.toml' \
--w 'packages_rs/nextclade/src' \
--w 'packages_rs/nextclade/Cargo.toml' \
+-w 'packages/nextclade-web/src' \
+-w 'packages/nextclade-web/Cargo.toml' \
+-w 'packages/nextclade/src' \
+-w 'packages/nextclade/Cargo.toml' \
 -w 'rust-toolchain.toml' \
 -w 'rustfmt.toml' \
 "
@@ -129,7 +129,7 @@ export FILES_TO_IGNORE="\
 -i '.cache' \
 -i '.vscode' \
 -i 'target/' \
--i 'packages_rs/nextclade-web/src/gen/' \
+-i 'packages/nextclade-web/src/gen/' \
 "
 
 export LINT_FIX="--fix --allow-staged"
@@ -471,11 +471,11 @@ elif [ "${BUILD}" == "1" ]; then
 elif [ "${SMOKE_TEST}" == "1" ]; then
   COMMAND="./tests/run-smoke-tests 'cargo run -q --target-dir='${BUILD_DIR_REL}' ${RUST_TARGET} ${RELEASE} --bin=nextclade'"
 elif [ "${WASM}" == "1" ]; then
-  COMMAND="bash -c \"set -euo pipefail && cd packages_rs/nextclade-web && yarn install && yarn wasm-${RELEASE}\""
+  COMMAND="bash -c \"set -euo pipefail && cd packages/nextclade-web && yarn install && yarn wasm-${RELEASE}\""
 elif [ "${WEB}" == "1" ]; then
   PORTS="-p 3000:3000"
   COMMAND=${COMMAND:=yarn install && yarn ${RELEASE}}
-  COMMAND="bash -c \"set -euo pipefail && cd packages_rs/nextclade-web && ${COMMAND}\""
+  COMMAND="bash -c \"set -euo pipefail && cd packages/nextclade-web && ${COMMAND}\""
 elif [ "${TEST}" == "1" ]; then
   PRETTY_TEST="( grep --color=always --line-buffered -vP \"running.*tests|\x1b\[32m.\x1b\(B\x1b\[m|^$|test result|TEST START\" || true )"
   COMMAND="cargo test --color=always -q --target-dir='${BUILD_DIR_REL}' ${RUST_TARGET} ${TEST_FLAGS} ${*:-} -- --nocapture --color=always | ${PRETTY_TEST} ${SUCCESS_OR_FAILURE}"

docs/dev/developer-guide.md

@@ -211,7 +211,7 @@ Install Node.js version 14+ (latest LTS release is recommended), by either downl
 5. Install NPM dependencies (once)
 
     ```bash
-    cd packages_rs/nextclade-web
+    cd packages/nextclade-web
     yarn install
     ```
 
@@ -220,11 +220,11 @@ Install Node.js version 14+ (latest LTS release is recommended), by either downl
 6. Build the WebAssembly module
 
     ```bash
-    cd packages_rs/nextclade-web
+    cd packages/nextclade-web
     yarn wasm-prod
     ```
 
-   This step might take a lot of time. The WebAssembly module and accompanying Typescript code should be been generated into  `packages_rs/nextclade-web/src/gen/`. The web application should be able to find it there.
+   This step might take a lot of time. The WebAssembly module and accompanying Typescript code should be been generated into  `packages/nextclade-web/src/gen/`. The web application should be able to find it there.
 
    Repeat this step every time you are touching Rust code.
 
@@ -235,7 +235,7 @@ Install Node.js version 14+ (latest LTS release is recommended), by either downl
    The development version can be built using:
 
     ```bash
-    cd packages_rs/nextclade-web
+    cd packages/nextclade-web
     yarn dev
     ```
 
@@ -250,7 +250,7 @@ Install Node.js version 14+ (latest LTS release is recommended), by either downl
 
    Open `http://localhost:8080/` in the browser.
 
-   The resulting HTML, CSS and JS files should be available under `packages_rs/nextclade-web/.build/production/web`.
+   The resulting HTML, CSS and JS files should be available under `packages/nextclade-web/.build/production/web`.
 
    Production build does not have automatic rebuild and reload. You need to do full rebuild on every code change.
 
@@ -321,7 +321,7 @@ For routine development, it is recommended to configure your text editor to see
 The web app is linted using [eslint](https://github.com/eslint/eslint) and [tsc](https://www.typescriptlang.org/docs/handbook/compiler-options.html) as a part of development command, but the same lints also be run separately:
 
 ```bash
-cd packages_rs/nextclade-web
+cd packages/nextclade-web
 yarn lint
 ```
 
@@ -340,7 +340,7 @@ cargo fmt --all
 Typescript:
 
 ```bash
-cd packages_rs/nextclade-web
+cd packages/nextclade-web
 yarn format:fix
 ```
 

scripts/build_on_vercel.sh

@@ -62,9 +62,9 @@ export PATH=/usr/lib/llvm-13/bin:${HOME}/.local/bin:${CARGO_HOME}/bin:${CARGO_HO
 
 symlink_to_cache ".build"
 symlink_to_cache ".cache"
-symlink_to_cache "packages_rs/nextclade-web/.build/production/tmp"
-symlink_to_cache "packages_rs/nextclade-web/.cache"
-symlink_to_cache "packages_rs/nextclade-web/node_modules"
+symlink_to_cache "packages/nextclade-web/.build/production/tmp"
+symlink_to_cache "packages/nextclade-web/.cache"
+symlink_to_cache "packages/nextclade-web/node_modules"
 
 # Install rustup and toolchain from rust-toolchain.toml, if not already in the cache
 if ! command cargo &>/dev/null; then
@@ -117,7 +117,7 @@ sed -i'' "s|PROD_ENABLE_STYLELINT=1|PROD_ENABLE_STYLELINT=0|g" .env
 
 sed -i'' "s|DATA_TRY_GITHUB_BRANCH=0|DATA_TRY_GITHUB_BRANCH=1|g" .env
 
-cd packages_rs/nextclade-web
+cd packages/nextclade-web
 
 yarn install --frozen-lockfile
 

scripts/cli_get_data_full_domain.sh

@@ -16,7 +16,7 @@ THIS_DIR="$(
 
 : "${1:?Branch name is required as the first argument.}"
 
-version=$(dasel select -p toml -s ".package.version" -f "packages_rs/nextclade-cli/Cargo.toml")
+version=$(dasel select -p toml -s ".package.version" -f "packages/nextclade-cli/Cargo.toml")
 prerel=$("${THIS_DIR}/semver" get prerel "${version}" | cut -d '.' -f 1)
 branch="${1}"
 

scripts/deploy_web.sh

@@ -8,7 +8,7 @@ trap "exit" INT
 
 export AWS_MAX_ATTEMPTS=10
 
-pushd "packages_rs/nextclade-web/.build/production/web" >/dev/null
+pushd "packages/nextclade-web/.build/production/web" >/dev/null
 
 # Precompress files
 pigz -kfrq .

scripts/publish_docker

@@ -41,7 +41,7 @@ declare -a BASE_IMAGES=(
   "debian"
 )
 
-version=$(dasel select -p toml -s ".package.version" -f "packages_rs/nextclade-cli/Cargo.toml")
+version=$(dasel select -p toml -s ".package.version" -f "packages/nextclade-cli/Cargo.toml")
 version_major=$("${THIS_DIR}/semver" get major "${version}")
 release_type=$("${THIS_DIR}/semver" get prerel "${version}" | cut -d '.' -f 1)
 release_type=${release_type:=latest}

scripts/publish_github

@@ -56,7 +56,7 @@ done
 [ -z "$repo" ] && echo "--repo is required" >/dev/stderr && exit 1
 [ -z "$git_sha" ] && echo "--git_sha is required" >/dev/stderr && exit 1
 
-version=$(dasel select -p toml -s ".package.version" -f "packages_rs/nextclade-cli/Cargo.toml")
+version=$(dasel select -p toml -s ".package.version" -f "packages/nextclade-cli/Cargo.toml")
 release_type=$("${THIS_DIR}/semver" get prerel "${version}" | cut -d '.' -f 1)
 prerelease_flag=${release_type:+--prerelease}
 

scripts/release

@@ -82,7 +82,7 @@ if [ "$1" == "cli" ]; then
 
   echo "Bumping package versions in 'Cargo.toml' files"
   cargo set-version --workspace --bump="${2:-}" >/dev/null
-  version=$(dasel select -r toml -s ".package.version" -f "packages_rs/nextclade/Cargo.toml")
+  version=$(dasel select -r toml -s ".package.version" -f "packages/nextclade/Cargo.toml")
 
   echo "Running \`cargo build\` to update 'Cargo.lock' file"
   cargo build --quiet >/dev/null
@@ -113,7 +113,7 @@ elif [ "$1" == "web" ]; then
     exit 1
   fi
 
-  pushd "packages_rs/nextclade-web" >/dev/null
+  pushd "packages/nextclade-web" >/dev/null
 
   if [[ "$2" =~ ^(major|minor|patch)$ ]]; then
     version=$(npm version "$2")

tests/functional/nextclade_run_args.t

@@ -7,10 +7,10 @@ Nextclade run: no output args
 
   $ ${NEXTCLADE} run \
   > --input-dataset='does not matter'
-  Error: 
+  Error:
      0: \x1b[91mWhen deducing output filenames\x1b[0m (esc)
      1: \x1b[91mNo output flags provided. (esc)
-  
+
         At least one of the following flags is required:
           --output-all
           --output-fasta
@@ -22,16 +22,16 @@ Nextclade run: no output args
           --output-translations
           --output-insertions
           --output-errors\x1b[0m (esc)
-  
+
   Location:
-     \x1b[35mpackages_rs/nextclade-cli/src/cli/nextclade_cli.rs\x1b[0m:\x1b[35m710\x1b[0m (esc)
-  
+     \x1b[35mpackages/nextclade-cli/src/cli/nextclade_cli.rs\x1b[0m:\x1b[35m710\x1b[0m (esc)
+
     \xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81 BACKTRACE \xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81 (esc)
      1: \x1b[32mmain\x1b[0m\x1b[90m<unknown>\x1b[0m (esc)
         at \x1b[35m<unknown source file>\x1b[0m:\x1b[35m<unknown line>\x1b[0m (esc)
      2: \x1b[32m__libc_start_main\x1b[0m\x1b[90m<unknown>\x1b[0m (esc)
         at \x1b[35m<unknown source file>\x1b[0m:\x1b[35m<unknown line>\x1b[0m (esc)
-  
+
   Run with COLORBT_SHOW_HIDDEN=1 environment variable to disable frame filtering.
   [1]
 
@@ -45,24 +45,24 @@ Nextclade run: no input dataset and no individual input flags
   $ ${NEXTCLADE} run \
   > --output-all='does not matter' \
   > 'does not matter'
-  Error: 
+  Error:
      0: \x1b[91mWhen `--input-dataset` is not specified, the following arguments are required: (esc)
-        --input-ref  
-        --input-tree  
-        --input-gene-map  
-        --input-qc-config  
-        --input-pcr-primers  
+        --input-ref
+        --input-tree
+        --input-gene-map
+        --input-qc-config
+        --input-pcr-primers
         --input-virus-properties\x1b[0m (esc)
-  
+
   Location:
-     \x1b[35mpackages_rs/nextclade-cli/src/dataset/dataset_download.rs\x1b[0m:\x1b[35m182\x1b[0m (esc)
-  
+     \x1b[35mpackages/nextclade-cli/src/dataset/dataset_download.rs\x1b[0m:\x1b[35m182\x1b[0m (esc)
+
     \xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81 BACKTRACE \xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81\xe2\x94\x81 (esc)
      1: \x1b[32mmain\x1b[0m\x1b[90m<unknown>\x1b[0m (esc)
         at \x1b[35m<unknown source file>\x1b[0m:\x1b[35m<unknown line>\x1b[0m (esc)
      2: \x1b[32m__libc_start_main\x1b[0m\x1b[90m<unknown>\x1b[0m (esc)
         at \x1b[35m<unknown source file>\x1b[0m:\x1b[35m<unknown line>\x1b[0m (esc)
-  
+
   Run with COLORBT_SHOW_HIDDEN=1 environment variable to disable frame filtering.
   [1]
 
@@ -78,7 +78,7 @@ Nextclade run: invalid value for --jobs
   > --input-dataset='does not matter' \
   > 'does not matter'
   error: Invalid value "Not an integer" for '--jobs <JOBS>': invalid digit found in string
-  
+
   For more information try --help
   [2]