Merge pull request #576 from nextstrain/fix/dataset-list-crash

fix: fix crash in dataset list command on macos
nextstrain · Oct 25, 2021 · 7b5cbce · 7b5cbce · vercel · Oct 25, 2021
2 parents b5f3cec + fce4f8d
commit 7b5cbce
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Showing 7 changed files with 58 additions and 44 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -43,7 +43,7 @@ jobs:
       - restore_cache:
           name: 'Restore previous checksum.txt from cache'
           keys:
-            - cache-nextclade-v6-builder-container-{{ checksum "checksum.current.txt" }}
+            - cache-nextclade-v7-builder-container-{{ checksum "checksum.current.txt" }}
 
       - run:
           name: 'Compare checksum.txt to cached one, halt if no changes'
@@ -80,7 +80,7 @@ jobs:
 
       - save_cache:
           name: 'Save new checksum.txt to cache'
-          key: cache-nextclade-v6-builder-container-{{ checksum "checksum.previous.txt" }}
+          key: cache-nextclade-v7-builder-container-{{ checksum "checksum.previous.txt" }}
           paths:
             - checksum.previous.txt
 
@@ -101,7 +101,7 @@ jobs:
       - restore_cache:
           name: 'Restore WebAssembly module build cache'
           keys:
-            - cache-nextclade-v6-web-wasm-{{ arch }}-{{ checksum "conanfile.wasm.txt" }}
+            - cache-nextclade-v7-web-wasm-{{ arch }}-{{ checksum "conanfile.wasm.txt" }}
 
       - run:
           name: 'Build WebAssembly module'
@@ -112,14 +112,14 @@ jobs:
 
       - save_cache:
           name: 'Save WebAssembly module build cache'
-          key: cache-nextclade-v6-web-wasm-{{ arch }}-{{ checksum "conanfile.wasm.txt" }}
+          key: cache-nextclade-v7-web-wasm-{{ arch }}-{{ checksum "conanfile.wasm.txt" }}
           paths:
             - .cache
 
       - restore_cache:
           name: 'Restore web application build cache'
           keys:
-            - cache-nextclade-v6-web-js-{{ arch }}-{{ checksum "packages/web/yarn.lock" }}
+            - cache-nextclade-v7-web-js-{{ arch }}-{{ checksum "packages/web/yarn.lock" }}
 
       - run:
           name: 'Build web application'
@@ -128,7 +128,7 @@ jobs:
 
       - save_cache:
           name: 'Save web application build cache'
-          key: cache-nextclade-v6-web-js-{{ arch }}-{{ checksum "packages/web/yarn.lock" }}
+          key: cache-nextclade-v7-web-js-{{ arch }}-{{ checksum "packages/web/yarn.lock" }}
           paths:
             - packages/web/.cache
             - packages/web/.build/production/tmp/cache
@@ -188,7 +188,7 @@ jobs:
       - restore_cache:
           name: 'Restore build cache'
           keys:
-            - cache-nextclade-v6-cache-{{ arch }}-{{ checksum "conanfile.txt" }}
+            - cache-nextclade-v7-cache-{{ arch }}-{{ checksum "conanfile.txt" }}
 
       - run:
           name: 'Run "Builder" container'
@@ -198,7 +198,7 @@ jobs:
 
       - save_cache:
           name: 'Save build cache'
-          key: cache-nextclade-v6-cache-{{ arch }}-{{ checksum "conanfile.txt" }}
+          key: cache-nextclade-v7-cache-{{ arch }}-{{ checksum "conanfile.txt" }}
           paths:
             - .cache
 
@@ -242,42 +242,50 @@ jobs:
       - restore_cache:
           name: 'Restore homebrew cache'
           keys:
-            - cache-nextclade-v6-homebrew-{{ arch }}-{{ checksum "Brewfile" }}
+            - cache-nextclade-v7-homebrew-{{ arch }}-{{ checksum "Brewfile" }}
 
       - run:
           name: 'Install build tools'
           command: |
             set -x
             brew bundle
+
+            mkdir -p .cache
+            python3 -m venv .cache/venv
+            source .cache/venv/bin/activate
+            pip3 install --upgrade -r requirements.txt
+
             conan profile new default --detect
+
           environment:
             HOMEBREW_NO_AUTO_UPDATE: 1
             CONAN_USER_HOME: '/Users/distiller/project/.cache'
 
       - save_cache:
           name: 'Save homebrew cache'
-          key: cache-nextclade-v6-homebrew-{{ arch }}-{{ checksum "Brewfile" }}
+          key: cache-nextclade-v7-homebrew-{{ arch }}-{{ checksum "Brewfile" }}
           paths:
             - '~/Library/Caches/Homebrew'
             - '/usr/local/Homebrew'
 
       - restore_cache:
           name: 'Restore build cache'
           keys:
-            - cache-nextclade-v6-cache-{{ arch }}-{{ checksum "conanfile.txt" }}-<< parameters.macos_arch >>
+            - cache-nextclade-v7-cache-{{ arch }}-{{ checksum "conanfile.txt" }}-<< parameters.macos_arch >>
 
       - run:
           name: Run macOS << parameters.macos_arch >> build
           command: |
-            echo "DATA_FULL_DOMAIN=${DATA_FULL_DOMAIN}" >> .env
+            source .cache/venv/bin/activate
+            echo "DATA_FULL_DOMAIN=https://data.master.clades.nextstrain.org" >> .env
             make prod
           environment:
             CONAN_USER_HOME: '/Users/distiller/project/.cache'
             HOST_ARCH: << parameters.macos_arch >>
 
       - save_cache:
           name: 'Save build cache'
-          key: cache-nextclade-v6-cache-{{ arch }}-{{ checksum "conanfile.txt" }}-<< parameters.macos_arch >>
+          key: cache-nextclade-v7-cache-{{ arch }}-{{ checksum "conanfile.txt" }}-<< parameters.macos_arch >>
           paths:
             - .cache
 
@@ -291,36 +299,36 @@ jobs:
           path: .out/bin/nextclade-MacOS-<< parameters.macos_arch >>
           destination: nextclade-MacOS-<< parameters.macos_arch >>
 
-      - run:
-          name: 'Publish binaries to GitHub Releases: MacOS-<< parameters.macos_arch >>'
-          command: |
-            OS=darwin ./scripts/download_github_release_tool.sh
-            ./scripts/publish_github_releases.sh
+#      - run:
+#          name: 'Publish binaries to GitHub Releases: MacOS-<< parameters.macos_arch >>'
+#          command: |
+#            OS=darwin ./scripts/download_github_release_tool.sh
+#            ./scripts/publish_github_releases.sh
 
 workflows:
   version: 2
   build:
     jobs:
-      - Update-Builder-Container:
-          <<: *major_branches_and_cli_release_only
-
-      - Build-Web:
-          context: nextclade_web_<< pipeline.git.branch >>
-          <<: *major_branches_only
-          requires:
-            - Update-Builder-Container
-
-      - Build-Linux-x86_64:
-          context: nextclade_cli_<< pipeline.git.branch >>
-          <<: *release_cli_only
-          requires:
-            - Update-Builder-Container
+#      - Update-Builder-Container:
+#          <<: *major_branches_and_cli_release_only
+#
+#      - Build-Web:
+#          context: nextclade_web_<< pipeline.git.branch >>
+#          <<: *major_branches_only
+#          requires:
+#            - Update-Builder-Container
+#
+#      - Build-Linux-x86_64:
+#          context: nextclade_cli_<< pipeline.git.branch >>
+#          <<: *release_cli_only
+#          requires:
+#            - Update-Builder-Container
 
       - Build-MacOS:
-          context: nextclade_cli_<< pipeline.git.branch >>
+#          context: nextclade_cli_<< pipeline.git.branch >>
           matrix:
             parameters:
               macos_arch:
                 - x86_64
-                - arm64
-          <<: *release_cli_only
+#                - arm64
+#          <<: *release_cli_only
diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,4 @@ paper/paper.pdf
 tmp
 build/
 *.bak
+Brewfile.lock.json
diff --git a/Brewfile b/Brewfile
@@ -2,7 +2,6 @@ brew "autoconf"
 brew "automake"
 brew "ccache"
 brew "cmake"
-brew "conan"
 brew "coreutils"
 brew "cppcheck"
 brew "ghr"

diff --git a/conanfile.txt b/conanfile.txt
@@ -6,7 +6,7 @@ cli11/1.9.1
 cxxopts/2.2.1
 date/3.0.1
 fast-cpp-csv-parser/20191004
-fmt/7.1.3
+fmt/8.0.1
 ghc-filesystem/1.4.0
 gtest/1.10.0
 jemalloc/5.2.1@local/stable

diff --git a/docs/dev/developers-guide-cli.md b/docs/dev/developers-guide-cli.md
@@ -55,14 +55,19 @@ The easiest way to start the development is to use the included docker container
     💡 Quick install for macOS  (click to expand)
     </summary>
 
-    You need to install XCode command line tools. After that you can install remaining required dependencies using [Homebrew](https://brew.sh/) and pip
+    You need to install XCode command line tools. After that you can install remaining required dependencies using [Homebrew](https://brew.sh/) and pip (into a Python virtual environment)
 
     ```
     xcode-select --install
 
     cd nextclade
     brew bundle --file=Brewfile
 
+    mkdir -p .cache
+    python3 -m venv .cache/venv
+    source .cache/venv/bin/activate
+    pip3 install --upgrade -r requirements.txt
+
     ```
     </details>
     </p>

diff --git a/packages/nextclade_common/src/datasets.cpp b/packages/nextclade_common/src/datasets.cpp
@@ -347,7 +347,9 @@ namespace Nextclade {
   }
 
   std::string formatDatasets(const std::vector<Dataset>& datasets, bool verbose /* = false */) {
-    fmt::memory_buffer buf;
+    fmt::memory_buffer bufRaw;
+    auto buf = std::back_inserter(bufRaw);
+
     for (const auto& dataset : datasets) {
       fmt::format_to(buf, "Dataset\n");
       fmt::format_to(buf, "-------\n");
@@ -369,7 +371,7 @@ namespace Nextclade {
 
       auto numRefs = std::to_string(dataset.datasetRefs.size());
       fmt::format_to(buf, "Specific reference sequences ({:}):\n", numRefs);
-      fmt::format_to(buf, "-----------------------------" + std::string{"-", numRefs.size() + 3} + "\n\n");
+      // fmt::format_to(buf, "-----------------------------" + std::string{"-", numRefs.size() + 3} + "\n\n");
 
       for (const auto& datasetRef : dataset.datasetRefs) {
         const auto& ref = datasetRef.reference;
@@ -394,7 +396,6 @@ namespace Nextclade {
 
         auto numTags = std::to_string(datasetRef.versions.size());
         fmt::format_to(buf, "    Specific versions ({:}):\n", datasetRef.versions.size());
-        fmt::format_to(buf, "    ------------------" + std::string{"-", numTags.size() + 3} + "\n\n");
 
         for (const auto& version : datasetRef.versions) {
           fmt::format_to(buf, "        Version\n");
@@ -441,7 +442,7 @@ namespace Nextclade {
       }
       fmt::format_to(buf, "\n");
     }
-    return fmt::to_string(buf);
+    return fmt::to_string(bufRaw);
   }
 
 

diff --git a/scripts/build_locally.sh b/scripts/build_locally.sh
@@ -787,9 +787,9 @@ pushd "${BUILD_DIR}" > /dev/null
     print 30 "Install executable";
     cmake --install "${BUILD_DIR}" --config "${CMAKE_BUILD_TYPE}" --strip
 
-    strip_executable "${NEXTALIGN_CLI}"
+#    strip_executable "${NEXTALIGN_CLI}"
 
-    strip_executable "${NEXTCLADE_CLI}"
+#    strip_executable "${NEXTCLADE_CLI}"
 
   fi