IMP: vscode-specific project structuring (#6)

bin/bootstrap_git_repos.py

@@ -0,0 +1,54 @@
+import json
+import os
+import subprocess
+
+from qiime2_projects import PROJECTS as Q2_PROJECTS
+from mds_projects import PROJECTS as MDS_PROJECTS
+from personal_projects import PROJECTS as PERSONAL_PROJECTS
+
+
+def fetch_projects(projects, base_fp, remotes):
+    for org, repos in projects.items():
+        base_fp = os.path.join('~', 'projects', base_fp)
+        base_fp = os.path.expanduser(base_fp)
+
+        for repo in repos:
+            print('repo: %s/%s' % (org, repo))
+
+            repo_fp = os.path.join(base_fp, repo)
+            repo_fp = os.path.expanduser(repo_fp)
+            if not os.path.isdir(repo_fp):
+                url = 'https://github.com/%s/%s' % (org, repo)
+                subprocess.run(['git', 'clone', url, repo_fp])
+                subprocess.run(['git', 'remote', 'rename', 'origin', org],
+                               cwd=repo_fp)
+            for remote in remotes:
+                url = 'https://github.com/%s/%s' % (remote, repo)
+                try:
+                    subprocess.run(['git', 'remote', 'add', remote, url],
+                                   cwd=repo_fp, check=True,
+                                   capture_output=True)
+                except subprocess.CalledProcessError as e:
+                    msg = 'remote %s already exists' % (remote, )
+                    if msg not in str(e.stderr):
+                        raise
+
+                try:
+                    subprocess.run(['git', 'fetch', remote],
+                                   cwd=repo_fp, check=True,
+                                   capture_output=True)
+                except subprocess.CalledProcessError as e:
+                    if url not in str(e.stderr):
+                        raise
+                    else:
+                        subprocess.run(['git', 'remote', 'remove', remote],
+                                       cwd=repo_fp)
+
+
+if __name__ == '__main__':
+    remotes = ['thermokarst', 'ebolyen', 'gregcaporaso', 'ChrisKeefe',
+               'Oddant1', 'nbokulich', 'andrewsanchez', 'David-Rod']
+
+    fetch_projects(Q2_PROJECTS, 'qiime2', remotes)
+    fetch_projects(MDS_PROJECTS, 'mds', [])
+    fetch_projects(PERSONAL_PROJECTS, 'personal', [])

bin/generate_vscode_workspaces.py

@@ -0,0 +1,57 @@
+import json
+import os
+
+from qiime2_projects import PROJECTS as Q2_PROJECTS
+from mds_projects import PROJECTS as MDS_PROJECTS
+from personal_projects import PROJECTS as PERSONAL_PROJECTS
+
+
+def render_vscode_workspace(projects, project_name, output_fp,
+                            include_dotfiles=True, extra_dirs=None):
+    folders = []
+    for org, repos in projects.items():
+        for repo in repos:
+            fp = os.path.join('~', 'projects', project_name, repo)
+            fp = os.path.expanduser(fp)
+            folders.append({'name': repo.lower(),
+                            'path': fp})
+
+    if include_dotfiles:
+        dotfile_fp = os.path.join(os.sep, 'Users', 'matthew', '.dotfiles')
+        folders.append({'name': 'dotfiles',
+                        'path': dotfile_fp})
+
+    if extra_dirs is not None:
+        for name, path in extra_dirs.items():
+            fp = os.path.join('~', 'projects', project_name, path)
+            fp = os.path.expanduser(fp)
+            folders.append({'name': name,
+                            'path': fp})
+
+    with open(output_fp, 'w') as fh:
+        json.dump({'folders': sorted(folders, key=lambda x: x['name'])},
+                  fh, sort_keys=True, indent=4)
+
+
+if __name__ == '__main__':
+    def qws(ws_number: int):
+        return render_vscode_workspace(
+        Q2_PROJECTS,
+        'qiime2',
+        os.path.join('vscode', 'qiime2-%d.code-workspace' % (ws_number, )),
+        extra_dirs={'data': 'data'},
+    )
+
+    [qws(i) for i in range(1, 4)]
+
+    render_vscode_workspace(
+        MDS_PROJECTS,
+        'mds',
+        os.path.join('vscode', 'mds.code-workspace'),
+    )
+
+    render_vscode_workspace(
+        PERSONAL_PROJECTS,
+        'personal',
+        os.path.join('vscode', 'personal.code-workspace'),
+    )

bin/mds_projects.py

@@ -0,0 +1,10 @@
+PROJECTS = {
+    'thermokarst': [
+        'ccdb-api',
+        'ccdb-web',
+        'tucotuco',
+        'fathm',
+        'hibernators',
+        'hibernators-web',
+    ],
+}

bin/personal_projects.py

@@ -0,0 +1,5 @@
+PROJECTS = {
+    'thermokarst': [
+        'elixir-class',
+    ],
+}

bin/qiime2_projects.py

@@ -0,0 +1,77 @@
+PROJECTS = {
+    'qiime2': [
+        'Keemei',
+        'action-library-packaging',
+        'busywork',
+        'data302',
+        'dev-docs',
+        'discourse-unhandled-tagger',
+        'docs',
+        'environment-files',
+        'library',
+        'logos',
+        'paper2',
+        'q2-alignment',
+        'q2-composition',
+        'q2-cutadapt',
+        'q2-dada2',
+        'q2-deblur',
+        'q2-demux',
+        'q2-diversity',
+        'q2-diversity-lib',
+        'q2-emperor',
+        'q2-feature-classifier',
+        'q2-feature-table',
+        'q2-fragment-insertion',
+        'q2-gneiss',
+        'q2-longitudinal',
+        'q2-metadata',
+        'q2-mystery-stew',
+        'q2-phylogenomics',
+        'q2-phylogeny',
+        'q2-quality-control',
+        'q2-quality-filter',
+        'q2-sample-classifier',
+        'q2-shogun',
+        'q2-taxa',
+        'q2-types',
+        'q2-vsearch',
+        'q2cli',
+        'q2cwl',
+        'q2galaxy',
+        'q2studio',
+        'q2templates',
+        'q2view',
+        'qiime2',
+        'qiime2.github.io',
+        'template-repo',
+        'view.qiime2.org',
+        'vm-playbooks',
+        'workshop-playbooks',
+        'workshops.qiime2.org',
+    ],
+
+    'caporaso-lab': [
+        'caporaso-lab.github.io',
+        'pretrained-feature-classifiers',
+    ],
+
+    'gregcaporaso': [
+        'caporaso-lab-secrets',
+        'qiime2-meta-figures',
+    ],
+
+    'biocore': [
+        'scikit-bio',
+        'deblur',
+    ],
+
+    'thermokarst': [
+        'q2-no-op',
+        'busywork2_action_playground',
+    ],
+
+ 'bioconda': [
+        'bioconda-recipes',
+    ]
+}