From f80d8e2ef8f8bc3e5442b0a7f5475145aa187bbb Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Thu, 8 Feb 2024 23:06:54 +0100 Subject: [PATCH] chore: find & replace packages_rs -> packages Preparation for mv packages_rs packages --- .github/dependabot.yml | 2 +- .github/workflows/cli.yml | 2 +- .github/workflows/web.yml | 14 +++++------ .gitignore | 4 ++-- Cargo.toml | 5 ++-- README.md | 2 +- docker/dev | 14 +++++------ docs/dev/developer-guide.md | 14 +++++------ scripts/build_on_vercel.sh | 8 +++---- scripts/cli_get_data_full_domain.sh | 2 +- scripts/deploy_web.sh | 2 +- scripts/publish_docker | 2 +- scripts/publish_github | 2 +- scripts/release | 4 ++-- tests/functional/nextclade_run_args.t | 34 +++++++++++++-------------- 15 files changed, 55 insertions(+), 56 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index b7e618637..09b75077f 100644 --- a/.github/dependabot.yml +++ b/.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: diff --git a/.github/workflows/cli.yml b/.github/workflows/cli.yml index 0d4cf127a..fa52501d9 100644 --- a/.github/workflows/cli.yml +++ b/.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 [[ "$version" =~ (rc|beta|alpha) ]]; then export DATA_FULL_DOMAIN="https://data.master.clades.nextstrain.org/v3" fi diff --git a/.github/workflows/web.yml b/.github/workflows/web.yml index 5311f6af7..f90917c89 100644 --- a/.github/workflows/web.yml +++ b/.github/workflows/web.yml @@ -83,7 +83,7 @@ jobs: path: | .build/ .cache/docker/.cargo - packages_rs/nextclade-web/.build/docker + packages/nextclade-web/.build/docker key: cache-v1-cargo-${{ 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'); \ diff --git a/.gitignore b/.gitignore index 56dcedeea..80bd5a158 100644 --- a/.gitignore +++ b/.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* diff --git a/Cargo.toml b/Cargo.toml index 67a14cec4..e6b2a9424 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,10 +1,9 @@ [workspace] members = [ - "packages_rs/*", + "packages/*", ] exclude = [ - "packages_rs/3rdparty", - "packages_rs/tree-builder-prototype" + "packages/3rdparty", ] diff --git a/README.md b/README.md index 4e7d46b17..8cb1960a6 100644 --- a/README.md +++ b/README.md @@ -109,7 +109,7 @@ by Nextstrain team package.json version diff --git a/docker/dev b/docker/dev index 6d900bcd7..454cdace0 100755 --- a/docker/dev +++ b/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}" diff --git a/docs/dev/developer-guide.md b/docs/dev/developer-guide.md index 986be5937..f5ee68f71 100644 --- a/docs/dev/developer-guide.md +++ b/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 ``` diff --git a/scripts/build_on_vercel.sh b/scripts/build_on_vercel.sh index e28133150..5a48830f7 100755 --- a/scripts/build_on_vercel.sh +++ b/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 diff --git a/scripts/cli_get_data_full_domain.sh b/scripts/cli_get_data_full_domain.sh index 0cbe33c6a..fbdc9eea3 100755 --- a/scripts/cli_get_data_full_domain.sh +++ b/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}" diff --git a/scripts/deploy_web.sh b/scripts/deploy_web.sh index 28eeafc14..f691c4554 100755 --- a/scripts/deploy_web.sh +++ b/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 . diff --git a/scripts/publish_docker b/scripts/publish_docker index feda5d98a..e57be2b68 100755 --- a/scripts/publish_docker +++ b/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=${release_type:=latest} diff --git a/scripts/publish_github b/scripts/publish_github index 70ca5d510..177d02f18 100755 --- a/scripts/publish_github +++ b/scripts/publish_github @@ -56,7 +56,7 @@ done [ -z "$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} diff --git a/scripts/release b/scripts/release index e80d5c623..e92423f6a 100755 --- a/scripts/release +++ b/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") diff --git a/tests/functional/nextclade_run_args.t b/tests/functional/nextclade_run_args.t index 0f924b967..b9a11229b 100644 --- a/tests/functional/nextclade_run_args.t +++ b/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\x1b[0m (esc) at \x1b[35m\x1b[0m:\x1b[35m\x1b[0m (esc) 2: \x1b[32m__libc_start_main\x1b[0m\x1b[90m\x1b[0m (esc) at \x1b[35m\x1b[0m:\x1b[35m\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\x1b[0m (esc) at \x1b[35m\x1b[0m:\x1b[35m\x1b[0m (esc) 2: \x1b[32m__libc_start_main\x1b[0m\x1b[90m\x1b[0m (esc) at \x1b[35m\x1b[0m:\x1b[35m\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 ': invalid digit found in string - + For more information try --help [2]