Merge pull request #58 from cbcrg/fix_release

Fix release process
cbcrg · Jun 7, 2023 · dbf6536 · dbf6536
2 parents c5b624f + ad700d4
commit dbf6536
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,4 +1,4 @@
-version: 2
+version: 2.1
 jobs:
   build:
     machine:
@@ -22,76 +22,142 @@ jobs:
           cbcrg/tcoffee-build-box:1.2 \
           bash -c 'tcoffee/build/build.sh env tcoffee; mv /root/sandbox /publish'
       - run: sudo chown -R $(id -u):$(id -g) ~/repo ~/publish
-      # tests and publish htmls 
-      - run:
-          command: |
-            mv ~/publish/sandbox/build ~/tcoffee/docker/tcoffee
-            cd ~/tcoffee/docker/ && docker build -t xcoffee .
-            mkdir -p ~/publish/sandbox/test-results
-            (set +e
-            docker run -v ~/tcoffee:/root/tcoffee -v ~/publish/sandbox/test-results:/test-results xcoffee bash /root/tcoffee/docker/run-tests.sh
-            test_status=$?
-            set -x
-            ## Modified
-            ## rsync -avz -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/publish/sandbox/test-results/index.html ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/tests/test-results-linux-x64-$(date +"%Y-%m-%d-%H:%M").html
-            ## TODO seems like the path ~/publish/sandbox/test-results/index.html does not exists
-            # aws s3 cp ~/publish/sandbox/test-results/index.html s3://tcoffee-packages/tests/test-results-linux-x64-$(date +"%Y-%m-%d-%H:%M").html
-            [[ "$test_status" != 0 ]] && exit $test_status || true
-            )
-          no_output_timeout: 30m
+      - persist_to_workspace:
+          root: /home/circleci
+          paths:
+            - publish
+            - tcoffee
+  # tests and publish test htmls
+  test:
+    machine:
+      image: ubuntu-2004:202201-02
+    steps:
+    - checkout
+    - attach_workspace:
+        at: /home/circleci
+    - run:
+        command: |
+          mv ~/publish/sandbox/build ~/tcoffee/docker/tcoffee
+          cd ~/tcoffee/docker/ && docker build -t xcoffee .
+          mkdir -p ~/publish/sandbox/test-results
+          (set +e
+          docker run -v ~/tcoffee:/root/tcoffee -v ~/publish/sandbox/test-results:/test-results xcoffee bash /root/tcoffee/docker/run-tests.sh
+          test_status=$?
+          set -x
+          ## Modified
+          ## rsync -avz -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/publish/sandbox/test-results/index.html ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/tests/test-results-linux-x64-$(date +"%Y-%m-%d-%H:%M").html
+          ## TODO seems like the path ~/publish/sandbox/test-results/index.html does not exists
+          # aws s3 cp ~/publish/sandbox/test-results/index.html s3://tcoffee-packages/tests/test-results-linux-x64-$(date +"%Y-%m-%d-%H:%M").html
+          [[ "$test_status" != 0 ]] && exit $test_status || true
+          )
+          cd ~/ && docker save -o xcoffee.tar xcoffee
+        no_output_timeout: 30m
+    - persist_to_workspace:
+        root: /home/circleci
+        paths: 
+          - xcoffee.tar
 
-      # publish artifacts 
-      - run: |
-          #
-          # This section will publish onto the websites the various elements produced by "make distribution"
-          # Note that since the distribution is usually triggered by the "git push" in "make release", the basic elements (doc, source and binary of the machine in which make release was launched) should already be published
-          #
-          if [[ $RELEASE == 1 ]]; then MODE=Stable; else MODE=Beta; fi;
-          version=$(cat ~/publish/sandbox/.version);
-          macosx_bversion=$(cat ~/tcoffee/binaries/macosx/version_number.version);
-          linux_bversion=$(cat ~/tcoffee/binaries/linux/version_number.version);
-          cp ~/tcoffee/build/web-readme.txt ~/publish/sandbox/distributions/$MODE/$version/readme.txt
-          #
-          # Start publishing the latest release -- make sure the receiving directory is not empty before deleting its content 
-          ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/lib/version/version_number.version ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/$MODE/Latest;
-          ## ssh ec2-user@tcoffee.org "rm  ~/Dropbox/Public/public_html/Packages/$MODE/Latest/*;";
-          # Don't need to remove the content of the directory, sync --delete will do it
-          ### aws s3 rm s3://tcoffee-packages/Stable/Latest/ --recursive --exclude "";
-          ### aws s3 cp ~/tcoffee/lib/version/version_number.version s3://tcoffee-packages/$MODE/Latest/;
-          ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/publish/sandbox/distributions/$MODE/$version/* ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/$MODE/Latest;
-          aws s3 sync ~/publish/sandbox/distributions/$MODE/$version/ s3://tcoffee-packages/$MODE/Latest/ --delete;
-          aws s3 sync ~/publish/sandbox/distributions/$MODE/$version/ s3://tcoffee.org/Packages/$MODE/Latest/ --delete;
-          ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/docs/.html/* ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Projects/tcoffee/documentation/;
-          aws s3 sync ~/tcoffee/docs/.html s3://tcoffee.org/Projects/tcoffee/documentation;
-          #
-          #Published binaries into the binary dir -- in case the macosx is available, publish it as well -- This will be the case when the release is launched from a mac
-          ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/binaries/macosx/t_coffee ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion;
-          ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/binaries/linux/t_coffee ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
-          aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee-packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
-          aws s3 cp ~/tcoffee/binaries/linux/t_coffee s3://tcoffee-packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
-          aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee.org/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
-          aws s3 cp ~/tcoffee/binaries/linux/t_coffee s3://tcoffee.org/Packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
-          aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee.org/Packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
-          #
-          #Publish the various distribution files into archives
-          ## ssh ec2-user@tcoffee.org "cp -r ~/Dropbox/Public/public_html/Packages/$MODE/Latest/* ~/Dropbox/Public/public_html/Packages/Archives";
-          aws s3 cp s3://tcoffee-packages/$MODE/Latest/ s3://tcoffee-packages/Archives/ --recursive;
-          #
-          # tag and push latest  
-          docker login -u $DOCKER_USER -p $DOCKER_PASS
-          docker tag xcoffee cbcrg/tcoffee:latest;
-          docker push cbcrg/tcoffee:latest;
-          # push stable 
-          if [[ $RELEASE == 1 ]]; then
-          docker tag xcoffee cbcrg/tcoffee:stable;
-          docker push cbcrg/tcoffee:stable;
-          fi
-          # tag versions
-          version=$(cat ~/publish/sandbox/.version);
-          docker tag xcoffee cbcrg/tcoffee:$version;
-          docker push cbcrg/tcoffee:$version;
-          if [[ $RELEASE == 1 ]]; then
-          version+='_stable'
-          docker tag xcoffee cbcrg/tcoffee:$version;
-          docker push cbcrg/tcoffee:$version;
-          fi
+  # publish artifacts
+  publish:
+    machine:
+      image: ubuntu-2004:202201-02
+    steps:
+    - attach_workspace:
+        at: /home/circleci
+    - run: |
+        #
+        # This section will publish onto the websites the various elements produced by "make distribution"
+        # Note that since the distribution is usually triggered by the "git push" in "make release", the basic elements (doc, source and binary of the machine in which make release was launched) should already be published
+        #
+        if [[ $RELEASE == 1 ]]; then MODE=Stable; else MODE=Beta; fi;
+        version=$(cat ~/publish/sandbox/.version);
+        macosx_bversion=$(cat ~/tcoffee/binaries/macosx/version_number.version);
+        linux_bversion=$(cat ~/tcoffee/binaries/linux/version_number.version);
+        cp ~/tcoffee/build/web-readme.txt ~/publish/sandbox/distributions/$MODE/$version/readme.txt
+        #
+        # Start publishing the latest release -- make sure the receiving directory is not empty before deleting its content 
+        ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/lib/version/version_number.version ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/$MODE/Latest;
+        ## ssh ec2-user@tcoffee.org "rm  ~/Dropbox/Public/public_html/Packages/$MODE/Latest/*;";
+        # Don't need to remove the content of the directory, sync --delete will do it
+        ### aws s3 rm s3://tcoffee-packages/Stable/Latest/ --recursive --exclude "";
+        ### aws s3 cp ~/tcoffee/lib/version/version_number.version s3://tcoffee-packages/$MODE/Latest/;
+        ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/publish/sandbox/distributions/$MODE/$version/* ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/$MODE/Latest;
+        aws s3 sync ~/publish/sandbox/distributions/$MODE/$version/ s3://tcoffee-packages/$MODE/Latest/ --delete;
+        aws s3 sync ~/publish/sandbox/distributions/$MODE/$version/ s3://tcoffee.org/Packages/$MODE/Latest/ --delete;
+        ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/docs/.html/* ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Projects/tcoffee/documentation/;
+        aws s3 sync ~/tcoffee/docs/.html s3://tcoffee.org/Projects/tcoffee/documentation;
+        #
+        #Published binaries into the binary dir -- in case the macosx is available, publish it as well -- This will be the case when the release is launched from a mac
+        ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/binaries/macosx/t_coffee ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion;
+        ## rsync -avzr -e "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null" ~/tcoffee/binaries/linux/t_coffee ec2-user@tcoffee.org:~/Dropbox/Public/public_html/Packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
+        aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee-packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
+        aws s3 cp ~/tcoffee/binaries/linux/t_coffee s3://tcoffee-packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
+        aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee.org/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
+        aws s3 cp ~/tcoffee/binaries/linux/t_coffee s3://tcoffee.org/Packages/Binaries/tcoffee/linux/t_coffee.$linux_bversion;
+        aws s3 cp ~/tcoffee/binaries/macosx/t_coffee s3://tcoffee.org/Packages/Binaries/tcoffee/macosx/t_coffee.$macosx_bversion; # only if launched from mac
+        #
+        #Publish the various distribution files into archives
+        ## ssh ec2-user@tcoffee.org "cp -r ~/Dropbox/Public/public_html/Packages/$MODE/Latest/* ~/Dropbox/Public/public_html/Packages/Archives";
+        aws s3 cp s3://tcoffee-packages/$MODE/Latest/ s3://tcoffee-packages/Archives/ --recursive;
+        #
+
+  # tag and push docker latest
+  push_image:
+    machine:
+      image: ubuntu-2004:202201-02
+    steps:
+    - attach_workspace:
+        at: /home/circleci
+    - checkout
+    - run: |
+        docker load -i ~/xcoffee.tar
+        docker login -u $DOCKER_USER -p $DOCKER_PASS
+        docker tag xcoffee cbcrg/tcoffee:latest;
+        docker push cbcrg/tcoffee:latest;
+        # push stable 
+        if [[ $RELEASE == 1 ]]; then
+        docker tag xcoffee cbcrg/tcoffee:stable;
+        docker push cbcrg/tcoffee:stable;
+        fi
+        # tag versions
+        version=$(cat ~/publish/sandbox/.version);
+        docker tag xcoffee cbcrg/tcoffee:$version;
+        docker push cbcrg/tcoffee:$version;
+        if [[ $RELEASE == 1 ]]; then
+        version+='_stable'
+        docker tag xcoffee cbcrg/tcoffee:$version;
+        docker push cbcrg/tcoffee:$version;
+        fi
+
+# Workflow declaration 
+# See here (https://stackoverflow.com/questions/66689847/executing-a-circleci-job-only-when-tag-matches-a-certain-pattern)
+# Another example https://goreleaser.com/ci/circle/
+workflows:
+  build_test_publish:
+    jobs:
+      - build:
+          filters:
+            tags:
+              only: /.*/
+      - test:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+      - publish:
+          requires:
+            - test
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /^V.*/
+      - push_image:
+          requires:
+            - publish
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /^V.*/
diff --git a/binaries/macosx/t_coffee b/binaries/macosx/t_coffee
diff --git a/docs/.html/.doctrees/doc2test.doctree b/docs/.html/.doctrees/doc2test.doctree
diff --git a/docs/.html/.doctrees/environment.pickle b/docs/.html/.doctrees/environment.pickle
diff --git a/docs/.html/.doctrees/index.doctree b/docs/.html/.doctrees/index.doctree
diff --git a/docs/.html/.doctrees/page-example.doctree b/docs/.html/.doctrees/page-example.doctree
diff --git a/docs/.html/.doctrees/tcoffee_citations_references.doctree b/docs/.html/.doctrees/tcoffee_citations_references.doctree
diff --git a/docs/.html/.doctrees/tcoffee_contacts_adresses.doctree b/docs/.html/.doctrees/tcoffee_contacts_adresses.doctree
diff --git a/docs/.html/.doctrees/tcoffee_faq.doctree b/docs/.html/.doctrees/tcoffee_faq.doctree
diff --git a/docs/.html/.doctrees/tcoffee_installation.doctree b/docs/.html/.doctrees/tcoffee_installation.doctree
diff --git a/docs/.html/.doctrees/tcoffee_license.doctree b/docs/.html/.doctrees/tcoffee_license.doctree
diff --git a/docs/.html/.doctrees/tcoffee_main_documentation.doctree b/docs/.html/.doctrees/tcoffee_main_documentation.doctree
diff --git a/docs/.html/.doctrees/tcoffee_quickstart.doctree b/docs/.html/.doctrees/tcoffee_quickstart.doctree
diff --git a/docs/.html/.doctrees/tcoffee_quickstart_regressive.doctree b/docs/.html/.doctrees/tcoffee_quickstart_regressive.doctree
diff --git a/docs/.html/.doctrees/tcoffee_release_guide.doctree b/docs/.html/.doctrees/tcoffee_release_guide.doctree
diff --git a/docs/.html/.doctrees/tcoffee_release_notes.doctree b/docs/.html/.doctrees/tcoffee_release_notes.doctree
diff --git a/docs/.html/.doctrees/tcoffee_technical_documentation.doctree b/docs/.html/.doctrees/tcoffee_technical_documentation.doctree
diff --git a/docs/.html/.doctrees/tcoffee_tutorials.doctree b/docs/.html/.doctrees/tcoffee_tutorials.doctree
diff --git a/docs/.html/.doctrees/tcoffee_webserver.doctree b/docs/.html/.doctrees/tcoffee_webserver.doctree
diff --git a/docs/.html/_static/basic.css b/docs/.html/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 450px;
+    min-width: 360px;
     max-width: 800px;
 }
 
@@ -237,16 +237,6 @@ a.headerlink {
     visibility: hidden;
 }
 
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
-}
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -334,13 +324,15 @@ aside.sidebar {
 p.sidebar-title {
     font-weight: bold;
 }
-
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
-
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -379,13 +371,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -428,10 +424,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.footnote td, table.footnote th {
-    border: 0 !important;
-}
-
 th {
     text-align: left;
     padding-right: 5px;
@@ -614,20 +606,26 @@ ol.simple p,
 ul.simple p {
     margin-bottom: 0;
 }
-
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -644,10 +642,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -757,6 +751,7 @@ span.pre {
     -ms-hyphens: none;
     -webkit-hyphens: none;
     hyphens: none;
+    white-space: nowrap;
 }
 
 div[class*="highlight-"] {