Merge branch 'componentscommand' of https://github.com/mirpedrol/tools …

…into componentscommand
nf-core · Nov 8, 2022 · 47dacd5 · 47dacd5
2 parents 5d598f2 + 4eae12d
commit 47dacd5
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Showing 15 changed files with 43 additions and 40 deletions.
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -48,7 +48,7 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -121,7 +121,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
           path: log.txt
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -51,7 +51,7 @@ jobs:
 
       - name: Upload log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
           path: log.txt
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -39,11 +39,11 @@ jobs:
           options: "--color"
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: python-isort
-        uses: isort/isort-action@v0.1.0
+        uses: isort/isort-action@v1.0.0
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -18,7 +18,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -32,7 +32,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -77,11 +77,11 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: python-isort
-        uses: isort/isort-action@v0.1.0
+        uses: isort/isort-action@v1.1.0
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -27,7 +27,7 @@ jobs:
           else
             curl -O https://nf-co.re/pipeline_names.json
           fi
-          echo "::set-output name=matrix::$(cat pipeline_names.json)"
+          echo "name=matrix::$(cat pipeline_names.json)" >> $GITHUB_OUTPUT
 
   sync:
     needs: get-pipelines
@@ -78,7 +78,7 @@ jobs:
 
       - name: Upload sync log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: sync_log_${{ matrix.pipeline }}
           path: sync_log_${{ matrix.pipeline }}.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,7 +25,9 @@
 - Run tests with Python 3.11 ([#1970](https://github.com/nf-core/tools/pull/1970))
 - Bump promoted Python version from 3.7 to 3.8 ([#1971](https://github.com/nf-core/tools/pull/1971))
 - Fix incorrect file deletion in `nf-core launch` when `--params_in` has the same name as `--params_out`
+- Updated GitHub actions ([#1998](https://github.com/nf-core/tools/pull/1998), [#2001](https://github.com/nf-core/tools/pull/2001))
 - Track from where modules and subworkflows are installed ([#1999](https://github.com/nf-core/tools/pull/1999))
+- Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand ([#2000](https://github.com/nf-core/tools/pull/2000))
 
 ### Modules
 

diff --git a/nf_core/components/components_install.py b/nf_core/components/components_install.py
@@ -100,4 +100,4 @@ def clean_modules_json(component, component_type, modules_repo, modules_json):
                         f"Removing {component_type[:-1]} '{modules_repo.repo_path}/{component}' from repo '{repo_to_remove}' from modules.json"
                     )
                     modules_json.remove_entry(component_type, component, repo_to_remove, modules_repo.repo_path)
-                    return component_values["installed"]
+                    return component_values["installed_by"]
diff --git a/nf_core/create.py b/nf_core/create.py
@@ -3,7 +3,6 @@
 organization's specification based on a template.
 """
 import configparser
-import imghdr
 import logging
 import os
 import random
@@ -13,6 +12,7 @@
 import time
 from pathlib import Path
 
+import filetype
 import git
 import jinja2
 import questionary
@@ -492,7 +492,7 @@ def download_pipeline_logo(self, url, img_fn):
             with open(img_fn, "wb") as fh:
                 fh.write(r.content)
             # Check that the file looks valid
-            image_type = imghdr.what(img_fn)
+            image_type = filetype.guess(img_fn).extension
             if image_type != "png":
                 log.error(f"Logo from the website didn't look like an image: '{image_type}'")
                 continue

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
@@ -277,7 +277,7 @@ def determine_module_branches_and_shas(self, install_dir, remote_url, modules):
                 repo_entry[module] = {
                     "branch": modules_repo.branch,
                     "git_sha": correct_commit_sha,
-                    "installed": "modules",
+                    "installed_by": "modules",
                 }
 
         # Clean up the modules we were unable to find the sha for
@@ -481,8 +481,8 @@ def check_up_to_date(self):
         If a module/subworkflow is installed but the entry in 'modules.json' is missing we iterate through
         the commit log in the remote to try to determine the SHA.
 
-        Check that we have the "installed" value in 'modules.json', otherwise add it.
-        Assume that the modules/subworkflows were installed by and nf-core command (don't track installed by subworkflows).
+        Check that we have the "installed_by" value in 'modules.json', otherwise add it.
+        Assume that the modules/subworkflows were installed by an nf-core command (don't track installed by subworkflows).
         """
         try:
             self.load()
@@ -517,13 +517,13 @@ def check_up_to_date(self):
         if len(subworkflows_missing_from_modules_json) > 0:
             self.resolve_missing_from_modules_json(subworkflows_missing_from_modules_json, "subworkflows")
 
-        # If the "installed" value is not present for modules/subworkflows, add it.
+        # If the "installed_by" value is not present for modules/subworkflows, add it.
         for repo, repo_content in self.modules_json["repos"].items():
             for component_type, dir_content in repo_content.items():
                 for install_dir, installed_components in dir_content.items():
                     for component, component_features in installed_components.items():
-                        if "installed" not in component_features:
-                            self.modules_json["repos"][repo][component_type][install_dir][component]["installed"] = [
+                        if "installed_by" not in component_features:
+                            self.modules_json["repos"][repo][component_type][install_dir][component]["installed_by"] = [
                                 component_type
                             ]
 
@@ -572,12 +572,12 @@ def update(self, modules_repo, module_name, module_version, installed_by, instal
         repo_modules_entry[module_name]["git_sha"] = module_version
         repo_modules_entry[module_name]["branch"] = branch
         try:
-            if installed_by not in repo_modules_entry[module_name]["installed"]:
-                repo_modules_entry[module_name]["installed"].append(installed_by)
+            if installed_by not in repo_modules_entry[module_name]["installed_by"]:
+                repo_modules_entry[module_name]["installed_by"].append(installed_by)
         except KeyError:
-            repo_modules_entry[module_name]["installed"] = [installed_by]
+            repo_modules_entry[module_name]["installed_by"] = [installed_by]
         finally:
-            repo_modules_entry[module_name]["installed"].extend(installed_by_log)
+            repo_modules_entry[module_name]["installed_by"].extend(installed_by_log)
 
         # Sort the 'modules.json' repo entries
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])
@@ -616,12 +616,12 @@ def update_subworkflow(
         repo_subworkflows_entry[subworkflow_name]["git_sha"] = subworkflow_version
         repo_subworkflows_entry[subworkflow_name]["branch"] = branch
         try:
-            if installed_by not in repo_subworkflows_entry[subworkflow_name]["installed"]:
-                repo_subworkflows_entry[subworkflow_name]["installed"].append(installed_by)
+            if installed_by not in repo_subworkflows_entry[subworkflow_name]["installed_by"]:
+                repo_subworkflows_entry[subworkflow_name]["installed_by"].append(installed_by)
         except KeyError:
-            repo_subworkflows_entry[subworkflow_name]["installed"] = [installed_by]
+            repo_subworkflows_entry[subworkflow_name]["installed_by"] = [installed_by]
         finally:
-            repo_subworkflows_entry[subworkflow_name]["installed"].extend(installed_by_log)
+            repo_subworkflows_entry[subworkflow_name]["installed_by"].extend(installed_by_log)
 
         # Sort the 'modules.json' repo entries
         self.modules_json["repos"] = nf_core.utils.sort_dictionary(self.modules_json["repos"])

diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "name=result::pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "name=result::fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -29,7 +29,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -99,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -8,17 +8,17 @@
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
-                        "installed": ["modules"]
+                        "installed_by": ["modules"]
                     }
                 }
             }

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,5 @@
 click
+filetype
 galaxy-tool-util
 GitPython
 jinja2

diff --git a/tests/modules/modules_json.py b/tests/modules/modules_json.py
@@ -41,7 +41,7 @@ def test_mod_json_update(self):
         NF_CORE_MODULES_DEFAULT_BRANCH
         == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"]
     )
-    assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed"]
+    assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"]
 
 
 def test_mod_json_create(self):