IMP: vscode-specific project structuring (#6)

.gitignore

@@ -0,0 +1,109 @@
+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python

.gitmodules

@@ -1,3 +1,4 @@
 [submodule "dotbot"]
 	path = dotbot
 	url = https://github.com/anishathalye/dotbot
+	ignore = dirty

README.md

@@ -18,7 +18,6 @@ $ nix-env -i \
   docker \
   git \
   htop \
-  mr \
   postgresql \
   reattach-to-user-namespace \
   silver-searcher \
@@ -28,13 +27,18 @@ $ nix-env -i \
   xz
 $ base16_ashes
 $ code --install-extension AndrsDC.base16-themes
+$ code --install-extension ecmel.vscode-html-css
+$ code --install-extension formulahendry.auto-close-tag
+$ code --install-extension hollowtree.vue-snippets
+$ code --install-extension JakeBecker.elixir-ls
+$ code --install-extension karigari.chat
 $ code --install-extension lextudio.restructuredtext
 $ code --install-extension ms-python.python
+$ code --install-extension ms-vscode.Go
+$ code --install-extension ms-vsliveshare.vsliveshare
+$ code --install-extension redhat.vscode-yaml
 $ code --install-extension vscodevim.vim
-$ code --install-extension alefragnani.project-manager
-$ code --install-extension donjayamanne.githistory
 $ code --install-extension wakatime.vscode-wakatime
-$ mr checkout
 $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
 $ sudo sh Miniconda3-latest-MacOSX-x86_64.sh -p /opt/miniconda3 -b
 $ sudo conda update conda

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',
+    ]
+}

dotbot

@@ -1 +1 @@
-Subproject commit ef558f85d917c7d2fb52c17db10f0996ef92cb3f
+Subproject commit 5d83f9e797b1950199e127a8196803f5e33e0916

git/gitconfig

@@ -2,7 +2,7 @@
     name = Matthew Dillon
     email = matthewrdillon@gmail.com
 [core]
-    editor = code --wait
+    editor = vim
     excludesfile = /Users/matthew/.gitignore_global
 [color]
     diff = auto

install

@@ -9,6 +9,7 @@ DOTBOT_BIN="bin/dotbot"
 BASEDIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 cd "${BASEDIR}"
+git -C "${DOTBOT_DIR}" submodule sync --quiet --recursive
 git submodule update --init --recursive "${DOTBOT_DIR}"
 
 "${BASEDIR}/${DOTBOT_DIR}/${DOTBOT_BIN}" -d "${BASEDIR}" -c "${CONFIG}" "${@}"

install.conf.yaml

@@ -1,17 +1,28 @@
-- clean: ['~']
+- clean:
+  - '~'
+
+- create:
+  - ~/projects/qiime2
+  - ~/projects/qiime2/data/moving-pictures
+  - ~/projects/mds
+  - ~/projects/personal
+
+- shell:
+  - python3 bin/generate_vscode_workspaces.py
+  - python3 bin/bootstrap_git_repos.py
 
 - link:
-    ~/.tmux.conf:                tmux.conf
+    ~/.tmux.conf: tmux.conf
-    ~/.gitconfig:                git/gitconfig
+    ~/.gitconfig: git/gitconfig
-    ~/.gitignore_global:         git/gitignore_global
+    ~/.gitignore_global: git/gitignore_global
-    ~/.psqlrc:                   psqlrc
+    ~/.npmrc: npmrc
-    ~/.zpreztorc:                zsh/zpreztorc
+    ~/.psqlrc: psqlrc
-    ~/.zlogin:                   zsh/zlogin
+    ~/.zpreztorc: zsh/zpreztorc
-    ~/.zlogout:                  zsh/zlogout
+    ~/.zlogin: zsh/zlogin
-    ~/.zprofile:                 zsh/zprofile
+    ~/.zlogout: zsh/zlogout
-    ~/.zshenv:                   zsh/zshenv
+    ~/.zprofile: zsh/zprofile
-    ~/.zshrc:                    zsh/zshrc
+    ~/.zshenv: zsh/zshenv
-    ~/.mrconfig:                 mrconfig
+    ~/.zshrc: zsh/zshrc
     ~/Library/Application Support/Code/User/settings.json:
       create: true
       path: vscode/settings.json
@@ -21,6 +32,8 @@
     ~/Library/Application Support/Code/User/tasks.json:
       create: true
       path: vscode/tasks.json
-    ~/Library/Application Support/Code/User/globalStorage/alefragnani.project-manager/projects.json:
+    ~/qiime2-1.code-workspace: vscode/qiime2-1.code-workspace
-      create: true
+    ~/qiime2-2.code-workspace: vscode/qiime2-2.code-workspace
-      path: vscode/projects.json
+    ~/qiime2-3.code-workspace: vscode/qiime2-3.code-workspace
+    ~/mds.code-workspace: vscode/mds.code-workspace
+    ~/personal.code-workspace: vscode/personal.code-workspace

metabin/generate_vscode_projects.py

@@ -1,97 +0,0 @@
-import json
-
-
-qiime2_projects = [
-    'Keemei',
-    'busywork',
-    'data.qiime2.org',
-    'dev-docs',
-    'discourse-unhandled-tagger',
-    'docs',
-    'environment-files',
-    'galaxy',
-    'library',
-    'logos',
-    '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-phylogeny',
-    'q2-quality-control',
-    'q2-quality-filter',
-    'q2-sample-classifier',
-    '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',
-]
-
-thermokarst_projects = [
-    'ccdb-api',
-    'ccdb-web',
-    'fathm',
-    'tucotuco',
-]
-
-cap_lab_projects = [
-    'caporaso-lab.github.io',
-    'pretrained-feature-classifiers',
-]
-
-gregcaporaso_projects = [
-    'caporaso-lab-secrets',
-    'qiime2-meta-figures',
-]
-
-projects = []
-
-def record(name, rootPath, group):
-    return {
-        'name': name,
-        'rootPath': rootPath,
-        'paths': [],
-        'group': group,
-        'enabled': True,
-    }
-
-Record = lambda x, y, z: record(x.lower(), '/'.join([y, x]), z)
-
-for proj in qiime2_projects:
-    projects.append(Record(proj, '$home/src/qiime2', 'qiime2'))
-
-for proj in thermokarst_projects:
-    projects.append(Record(proj, '$home/src/thermokarst', 'thermokarst'))
-
-for proj in cap_lab_projects:
-    projects.append(Record(proj, '$home/src/caporaso-lab', 'caporaso-lab'))
-
-for proj in gregcaporaso_projects:
-    projects.append(Record(proj, '$home/src/gregcaporaso', 'gregcaporaso'))
-
-projects.append(record('dotfiles', '$home/.dotfiles', ''))
-
-with open('vscode/projects.json', 'w') as fh:
-    json.dump(projects, fh, sort_keys=True, indent=4)

mrconfig

@@ -1,454 +0,0 @@
-### applied-bioinformatics
-[src/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics]
-checkout = git clone https://github.com/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics An-Introduction-To-Applied-Bioinformatics && \
-    cd An-Introduction-To-Applied-Bioinformatics && \
-    git remote rename origin applied-bioinformatics && \
-    git remote add thermokarst https://github.com/thermokarst/An-Introduction-To-Applied-Bioinformatics && \
-    git fetch thermokarst
-
-
-### biocore
-checkout = git clone https://github.com/biocore/deblur deblur && \
-    cd deblur && \
-    git remote rename origin biocore && \
-    git remote add thermokarst https://github.com/thermokarst/deblur && \
-    git fetch thermokarst
-
-checkout = git clone https://github.com/biocore/scikit-bio scikit-bio && \
-    cd scikit-bio && \
-    git remote rename origin biocore && \
-    git remote add ElDeveloper https://github.com/ElDeveloper/scikit-bio && \
-    git remote add ebolyen https://github.com/ebolyen/scikit-bio && \
-    git remote add wasade https://github.com/wasade/scikit-bio && \
-    git remote add thermokarst https://github.com/thermokarst/scikit-bio && \
-    git fetch thermokarst
-
-
-### caporaso-lab
-[src/caporaso-lab/SurveySync]
-checkout = git clone https://github.com/caporaso-lab/SurveySync SurveySync && \
-    cd SurveySync && \
-    git remote rename origin caporaso-lab && \
-    git remote add turanoo https://github.com/turanoo/SurveySync && \
-    git remote add thermokarst https://github.com/thermokarst/SurveySync && \
-    git fetch thermokarst
-
-[src/caporaso-lab/caporaso-lab.github.io]
-checkout = git clone https://github.com/caporaso-lab/caporaso-lab.github.io caporaso-lab.github.io && \
-    cd caporaso-lab.github.io && \
-    git remote rename origin caporaso-lab && \
-    git remote add thermokarst https://github.com/thermokarst/caporaso-lab.github.io && \
-    git fetch thermokarst
-
-[src/caporaso-lab/sc18-poster]
-checkout = git clone https://github.com/caporaso-lab/sc18-poster sc18-poster && \
-    cd sc18-poster && \
-    git remote rename origin caporaso-lab && \
-    git remote add thermokarst https://github.com/thermokarst/sc18-poster && \
-    git fetch thermokarst
-
-[src/caporaso-lab/pretrained-feature-classifiers]
-checkout = git clone https://github.com/caporaso-lab/pretrained-feature-classifiers pretrained-feature-classifiers && \
-    cd pretrained-feature-classifiers && \
-    git remote rename origin caporaso-lab && \
-    git remote add thermokarst https://github.com/thermokarst/pretrained-feature-classifiers && \
-    git fetch thermokarst
-
-
-### qiime2
-[src/qiime2/Keemei]
-checkout = git clone https://github.com/qiime2/Keemei Keemei && \
-    cd Keemei && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/Keemei && \
-    git fetch thermokarst
-
-[src/qiime2/busywork]
-checkout = git clone https://github.com/qiime2/busywork busywork && \
-    cd busywork && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/busywork && \
-    git fetch thermokarst
-
-[src/qiime2/data.qiime2.org]
-checkout = git clone https://github.com/qiime2/data.qiime2.org data.qiime2.org && \
-    cd data.qiime2.org && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/data.qiime2.org && \
-    git fetch thermokarst
-
-[src/qiime2/dev-docs]
-checkout = git clone https://github.com/qiime2/dev-docs dev-docs && \
-    cd dev-docs && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/dev-docs && \
-    git fetch thermokarst
-
-[src/qiime2/discourse-unhandled-tagger]
-checkout = git clone https://github.com/qiime2/discourse-unhandled-tagger discourse-unhandled-tagger && \
-    cd discourse-unhandled-tagger && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/discourse-unhandled-tagger && \
-    git fetch thermokarst
-
-[src/qiime2/docs]
-checkout = git clone https://github.com/qiime2/docs docs && \
-    cd docs && \
-    git remote rename origin qiime2 && \
-    git remote add ChrisKeefe https://github.com/ChrisKeefe/docs && \
-    git remote add antgonza https://github.com/antgonza/docs && \
-    git remote add cduvallet https://github.com/cduvallet/docs && \
-    git remote add ebolyen https://github.com/ebolyen/docs && \
-    git remote add nbokulich https://github.com/nbokulich/docs && \
-    git remote add turanoo https://github.com/turanoo/docs && \
-    git remote add gregcaporaso https://github.com/gregcaporaso/docs && \
-    git remote add thermokarst https://github.com/thermokarst/docs && \
-    git fetch thermokarst
-
-[src/qiime2/environment-files]
-checkout = git clone https://github.com/qiime2/environment-files environment-files && \
-    cd environment-files && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/environment-files && \
-    git fetch thermokarst
-
-[src/qiime2/library]
-checkout = git clone https://github.com/qiime2/library library && \
-    cd library && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/library && \
-    git fetch thermokarst
-
-[src/qiime2/logos]
-checkout = git clone https://github.com/qiime2/logos logos && \
-    cd logos && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/logos && \
-    git fetch thermokarst
-
-[src/qiime2/q2-alignment]
-checkout = git clone https://github.com/qiime2/q2-alignment q2-alignment && \
-    cd q2-alignment && \
-    git remote rename origin qiime2 && \
-    git remote add turanoo https://github.com/turanoo/q2-alignment && \
-    git remote add thermokarst https://github.com/thermokarst/q2-alignment && \
-    git fetch thermokarst
-
-[src/qiime2/q2-composition]
-checkout = git clone https://github.com/qiime2/q2-composition q2-composition && \
-    cd q2-composition && \
-    git remote rename origin qiime2 && \
-    git remote add nbokulich https://github.com/nbokulich/q2-composition && \
-    git remote add thermokarst https://github.com/thermokarst/q2-composition && \
-    git fetch thermokarst
-
-[src/qiime2/q2-cutadapt]
-checkout = git clone https://github.com/qiime2/q2-cutadapt q2-cutadapt && \
-    cd q2-cutadapt && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2-cutadapt && \
-    git remote add thermokarst https://github.com/thermokarst/q2-cutadapt && \
-    git fetch thermokarst
-
-[src/qiime2/q2-dada2]
-checkout = git clone https://github.com/qiime2/q2-dada2 q2-dada2 && \
-    cd q2-dada2 && \
-    git remote rename origin qiime2 && \
-    git remote add benjjneb https://github.com/benjjneb/q2-dada2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2-dada2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-dada2 && \
-    git fetch thermokarst
-
-[src/qiime2/q2-deblur]
-checkout = git clone https://github.com/qiime2/q2-deblur q2-deblur && \
-    cd q2-deblur && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-deblur && \
-    git fetch thermokarst
-
-[src/qiime2/q2-demux]
-checkout = git clone https://github.com/qiime2/q2-demux q2-demux && \
-    cd q2-demux && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-demux && \
-    git fetch thermokarst
-
-[src/qiime2/q2-diversity]
-checkout = git clone https://github.com/qiime2/q2-diversity q2-diversity && \
-    cd q2-diversity && \
-    git remote rename origin qiime2 && \
-    git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity && \
-    git remote add ElDeveloper https://github.com/ElDeveloper/q2-diversity && \
-    git remote add ebolyen https://github.com/ebolyen/q2-diversity && \
-    git remote add nbokulich https://github.com/nbokulich/q2-diversity && \
-    git remote add thermokarst https://github.com/thermokarst/q2-diversity && \
-    git fetch thermokarst
-
-[src/qiime2/q2-diversity-lib]
-checkout = git clone https://github.com/qiime2/q2-diversity-lib q2-diversity-lib && \
-    cd q2-diversity-lib && \
-    git remote rename origin qiime2 && \
-    git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity-lib && \
-    git remote add thermokarst https://github.com/thermokarst/q2-diversity-lib && \
-    git fetch thermokarst
-
-[src/qiime2/q2-emperor]
-checkout = git clone https://github.com/qiime2/q2-emperor q2-emperor && \
-    cd q2-emperor && \
-    git remote rename origin qiime2 && \
-    git remote add ElDeveloper https://github.com/ElDeveloper/q2-emperor && \
-    git remote add thermokarst https://github.com/thermokarst/q2-emperor && \
-    git fetch thermokarst
-
-[src/qiime2/q2-feature-classifier]
-checkout = git clone https://github.com/qiime2/q2-feature-classifier q2-feature-classifier && \
-    cd q2-feature-classifier && \
-    git remote rename origin qiime2 && \
-    git remote add nbokulich https://github.com/nbokulich/q2-feature-classifier && \
-    git remote add thermokarst https://github.com/thermokarst/q2-feature-classifier && \
-    git fetch thermokarst
-
-[src/qiime2/q2-feature-table]
-checkout = git clone https://github.com/qiime2/q2-feature-table q2-feature-table && \
-    cd q2-feature-table && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2-feature-table && \
-    git remote add gregcaporaso https://github.com/gregcaporaso/q2-feature-table && \
-    git remote add wasade https://github.com/wasade/q2-feature-table && \
-    git remote add thermokarst https://github.com/thermokarst/q2-feature-table && \
-    git fetch thermokarst
-
-[src/qiime2/q2-fragment-insertion]
-checkout = git clone https://github.com/qiime2/q2-fragment-insertion q2-fragment-insertion && \
-    cd q2-fragment-insertion && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-fragment-insertion && \
-    git fetch thermokarst
-
-[src/qiime2/q2-gneiss]
-checkout = git clone https://github.com/qiime2/q2-gneiss q2-gneiss && \
-    cd q2-gneiss && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-gneiss && \
-    git fetch thermokarst
-
-[src/qiime2/q2-longitudinal]
-checkout = git clone https://github.com/qiime2/q2-longitudinal q2-longitudinal && \
-    cd q2-longitudinal && \
-    git remote rename origin qiime2 && \
-    git remote add nbokulich https://github.com/nbokulich/q2-longitudinal && \
-    git remote add thermokarst https://github.com/thermokarst/q2-longitudinal && \
-    git fetch thermokarst
-
-[src/qiime2/q2-metadata]
-checkout = git clone https://github.com/qiime2/q2-metadata q2-metadata && \
-    cd q2-metadata && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-metadata && \
-    git fetch thermokarst
-
-[src/qiime2/q2-phylogeny]
-checkout = git clone https://github.com/qiime2/q2-phylogeny q2-phylogeny && \
-    cd q2-phylogeny && \
-    git remote rename origin qiime2 && \
-    git remote add mikerobeson https://github.com/mikerobeson/q2-phylogeny && \
-    git remote add thermokarst https://github.com/thermokarst/q2-phylogeny && \
-    git fetch thermokarst
-
-[src/qiime2/q2-quality-control]
-checkout = git clone https://github.com/qiime2/q2-quality-control q2-quality-control && \
-    cd q2-quality-control && \
-    git remote rename origin qiime2 && \
-    git remote add nbokulich https://github.com/nbokulich/q2-quality-control && \
-    git remote add thermokarst https://github.com/thermokarst/q2-quality-control && \
-    git fetch thermokarst
-
-[src/qiime2/q2-quality-filter]
-checkout = git clone https://github.com/qiime2/q2-quality-filter q2-quality-filter && \
-    cd q2-quality-filter && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-quality-filter && \
-    git fetch thermokarst
-
-[src/qiime2/q2-sample-classifier]
-checkout = git clone https://github.com/qiime2/q2-sample-classifier q2-sample-classifier && \
-    cd q2-sample-classifier && \
-    git remote rename origin qiime2 && \
-    git remote add BenKaehler https://github.com/BenKaehler/q2-sample-classifier && \
-    git remote add nbokulich https://github.com/nbokulich/q2-sample-classifier && \
-    git remote add thermokarst https://github.com/thermokarst/q2-sample-classifier && \
-    git fetch thermokarst
-
-[src/qiime2/q2-taxa]
-checkout = git clone https://github.com/qiime2/q2-taxa q2-taxa && \
-    cd q2-taxa && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-taxa && \
-    git fetch thermokarst
-
-[src/qiime2/q2-types]
-checkout = git clone https://github.com/qiime2/q2-types q2-types && \
-    cd q2-types && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-types && \
-    git fetch thermokarst
-
-[src/qiime2/q2-vsearch]
-checkout = git clone https://github.com/qiime2/q2-vsearch q2-vsearch && \
-    cd q2-vsearch && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2-vsearch && \
-    git fetch thermokarst
-
-[src/qiime2/q2cli]
-checkout = git clone https://github.com/qiime2/q2cli q2cli && \
-    cd q2cli && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2cli && \
-    git remote add turanoo https://github.com/turanoo/q2cli && \
-    git remote add thermokarst https://github.com/thermokarst/q2cli && \
-    git fetch thermokarst
-
-[src/qiime2/q2cwl]
-checkout = git clone https://github.com/qiime2/q2cwl q2cwl && \
-    cd q2cwl && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2cwl && \
-    git remote add thermokarst https://github.com/thermokarst/q2cwl && \
-    git fetch thermokarst
-
-[src/qiime2/q2galaxy]
-checkout = git clone https://github.com/qiime2/q2galaxy q2galaxy && \
-    cd q2galaxy && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2galaxy && \
-    git remote add thermokarst https://github.com/thermokarst/q2galaxy && \
-    git fetch thermokarst
-
-[src/qiime2/galaxy]
-checkout = git clone https://github.com/galaxyproject/galaxy galaxy && \
-    cd galaxy && \
-    git remote rename origin galaxyproject && \
-    git remote add ebolyen https://github.com/ebolyen/galaxy && \
-    git remote add thermokarst https://github.com/thermokarst/galaxy && \
-    git fetch thermokarst
-
-[src/qiime2/q2studio]
-checkout = git clone https://github.com/qiime2/q2studio q2studio && \
-    cd q2studio && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2studio && \
-    git fetch thermokarst
-
-[src/qiime2/q2templates]
-checkout = git clone https://github.com/qiime2/q2templates q2templates && \
-    cd q2templates && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/q2templates && \
-    git fetch thermokarst
-
-[src/qiime2/q2view]
-checkout = git clone https://github.com/qiime2/q2view q2view && \
-    cd q2view && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/q2view && \
-    git remote add turanoo https://github.com/turanoo/q2view && \
-    git remote add thermokarst https://github.com/thermokarst/q2view && \
-    git fetch thermokarst
-
-[src/qiime2/qiime2]
-checkout = git clone https://github.com/qiime2/qiime2 qiime2 && \
-    cd qiime2 && \
-    git remote rename origin qiime2 && \
-    git remote add ebolyen https://github.com/ebolyen/qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/qiime2 && \
-    git fetch thermokarst
-
-[src/qiime2/qiime2.github.io]
-checkout = git clone https://github.com/qiime2/qiime2.github.io qiime2.github.io && \
-    cd qiime2.github.io && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/qiime2.github.io && \
-    git fetch thermokarst
-
-[src/qiime2/template-repo]
-checkout = git clone https://github.com/qiime2/template-repo template-repo && \
-    cd template-repo && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/template-repo && \
-    git fetch thermokarst
-
-[src/qiime2/view.qiime2.org]
-checkout = git clone https://github.com/qiime2/view.qiime2.org view.qiime2.org && \
-    cd view.qiime2.org && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/view.qiime2.org && \
-    git fetch thermokarst
-
-[src/qiime2/vm-playbooks]
-checkout = git clone https://github.com/qiime2/vm-playbooks vm-playbooks && \
-    cd vm-playbooks && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/vm-playbooks && \
-    git fetch thermokarst
-
-[src/qiime2/workshop-playbooks]
-checkout = git clone https://github.com/qiime2/workshop-playbooks workshop-playbooks && \
-    cd workshop-playbooks && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/workshop-playbooks && \
-    git fetch thermokarst
-
-[src/qiime2/workshops.qiime2.org]
-checkout = git clone https://github.com/qiime2/workshops.qiime2.org workshops.qiime2.org && \
-    cd workshops.qiime2.org && \
-    git remote rename origin qiime2 && \
-    git remote add thermokarst https://github.com/thermokarst/workshops.qiime2.org && \
-    git fetch thermokarst
-
-
-### gregcaporaso
-[src/gregcaporaso/caporaso-lab-secrets]
-checkout = git clone https://github.com/gregcaporaso/caporaso-lab-secrets && \
-    cd caporaso-lab-secrets && \
-    git remote rename origin gregcaporaso && \
-    git remote add thermokarst https://github.com/thermokarst/caporaso-lab-secrets && \
-    git fetch thermokarst
-
-[src/gregcaporaso/qiime2-meta-figures]
-checkout = git clone https://github.com/gregcaporaso/qiime2-meta-figures && \
-    cd qiime2-meta-figures && \
-    git remote rename origin gregcaporaso && \
-    git remote add thermokarst https://github.com/thermokarst/qiime2-meta-figures && \
-    git fetch thermokarst
-
-[src/gregcaporaso/workshop-tutorials]
-checkout = git clone https://github.com/gregcaporaso/workshop-tutorials && \
-    cd workshop-tutorials && \
-    git remote rename origin gregcaporaso && \
-    git remote add thermokarst https://github.com/thermokarst/workshop-tutorials && \
-    git fetch thermokarst
-
-
-### thermokarst
-[src/thermokarst/ccdb-api]
-checkout = git clone https://github.com/thermokarst/ccdb-api && \
-    cd ccdb-api && \
-    git remote rename origin thermokarst
-
-[src/thermokarst/ccdb-web]
-checkout = git clone https://github.com/thermokarst/ccdb-web && \
-    cd ccdb-web && \
-    git remote rename origin thermokarst
-
-[src/thermokarst/fathm]
-checkout = git clone https://github.com/thermokarst/fathm && \
-    cd fathm && \
-    git remote rename origin thermokarst && \
-    git remote add gitlab https://gitlab.com/evalulogic/fathm.git && \
-    git fetch gitlab
-
-[src/thermokarst/tucotuco]
-checkout = git clone https://github.com/thermokarst/tucotuco && \
-    cd tucotuco && \
-    git remote rename origin thermokarst

npmrc

@@ -0,0 +1 @@
+prefix=~/.npm-packages

vscode/keybindings.json

@@ -3,5 +3,9 @@
         "key": "ctrl+w k",
         "command": "workbench.action.focusActiveEditorGroup",
         "when": "!editorFocus"
-    }
+    },
-]
+    {
+        "key": "cmd+m",
+        "command": "workbench.action.toggleMaximizedPanel"
+    },
+]

vscode/mds.code-workspace

@@ -0,0 +1,32 @@
+{
+    "folders": [
+        {
+            "name": "ccdb-api",
+            "path": "/Users/matthew/projects/mds/ccdb-api"
+        },
+        {
+            "name": "ccdb-web",
+            "path": "/Users/matthew/projects/mds/ccdb-web"
+        },
+        {
+            "name": "dotfiles",
+            "path": "/Users/matthew/.dotfiles"
+        },
+        {
+            "name": "fathm",
+            "path": "/Users/matthew/projects/mds/fathm"
+        },
+        {
+            "name": "hibernators",
+            "path": "/Users/matthew/projects/mds/hibernators"
+        },
+        {
+            "name": "hibernators-web",
+            "path": "/Users/matthew/projects/mds/hibernators-web"
+        },
+        {
+            "name": "tucotuco",
+            "path": "/Users/matthew/projects/mds/tucotuco"
+        }
+    ]
+}

vscode/personal.code-workspace

@@ -0,0 +1,12 @@
+{
+    "folders": [
+        {
+            "name": "dotfiles",
+            "path": "/Users/matthew/.dotfiles"
+        },
+        {
+            "name": "elixir-class",
+            "path": "/Users/matthew/projects/personal/elixir-class"
+        }
+    ]
+}

vscode/projects.json

@@ -1,380 +0,0 @@
-[
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "keemei",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/Keemei"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "busywork",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/busywork"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "data.qiime2.org",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/data.qiime2.org"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "dev-docs",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/dev-docs"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "discourse-unhandled-tagger",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/discourse-unhandled-tagger"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "docs",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/docs"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "environment-files",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/environment-files"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "galaxy",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/galaxy"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "library",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/library"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "logos",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/logos"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-alignment",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-alignment"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-composition",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-composition"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-cutadapt",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-cutadapt"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-dada2",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-dada2"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-deblur",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-deblur"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-demux",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-demux"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-diversity",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-diversity"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-diversity-lib",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-diversity-lib"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-emperor",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-emperor"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-feature-classifier",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-feature-classifier"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-feature-table",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-feature-table"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-fragment-insertion",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-fragment-insertion"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-gneiss",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-gneiss"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-longitudinal",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-longitudinal"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-metadata",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-metadata"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-phylogeny",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-phylogeny"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-quality-control",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-quality-control"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-quality-filter",
-        "paths": [],
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-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-taxa",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-taxa"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2-types",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-types"
-    },
-    {
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-        "group": "qiime2",
-        "name": "q2-vsearch",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2-vsearch"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2cli",
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-        "rootPath": "$home/src/qiime2/q2cli"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2cwl",
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-        "rootPath": "$home/src/qiime2/q2cwl"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2galaxy",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2galaxy"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2studio",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2studio"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2templates",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2templates"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "q2view",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/q2view"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "qiime2",
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-        "rootPath": "$home/src/qiime2/qiime2"
-    },
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-        "group": "qiime2",
-        "name": "qiime2.github.io",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/qiime2.github.io"
-    },
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-        "group": "qiime2",
-        "name": "template-repo",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/template-repo"
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-        "group": "qiime2",
-        "name": "view.qiime2.org",
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-    },
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-        "group": "qiime2",
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-        "paths": [],
-        "rootPath": "$home/src/qiime2/vm-playbooks"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "workshop-playbooks",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/workshop-playbooks"
-    },
-    {
-        "enabled": true,
-        "group": "qiime2",
-        "name": "workshops.qiime2.org",
-        "paths": [],
-        "rootPath": "$home/src/qiime2/workshops.qiime2.org"
-    },
-    {
-        "enabled": true,
-        "group": "thermokarst",
-        "name": "ccdb-api",
-        "paths": [],
-        "rootPath": "$home/src/thermokarst/ccdb-api"
-    },
-    {
-        "enabled": true,
-        "group": "thermokarst",
-        "name": "ccdb-web",
-        "paths": [],
-        "rootPath": "$home/src/thermokarst/ccdb-web"
-    },
-    {
-        "enabled": true,
-        "group": "thermokarst",
-        "name": "fathm",
-        "paths": [],
-        "rootPath": "$home/src/thermokarst/fathm"
-    },
-    {
-        "enabled": true,
-        "group": "thermokarst",
-        "name": "tucotuco",
-        "paths": [],
-        "rootPath": "$home/src/thermokarst/tucotuco"
-    },
-    {
-        "enabled": true,
-        "group": "caporaso-lab",
-        "name": "caporaso-lab.github.io",
-        "paths": [],
-        "rootPath": "$home/src/caporaso-lab/caporaso-lab.github.io"
-    },
-    {
-        "enabled": true,
-        "group": "caporaso-lab",
-        "name": "pretrained-feature-classifiers",
-        "paths": [],
-        "rootPath": "$home/src/caporaso-lab/pretrained-feature-classifiers"
-    },
-    {
-        "enabled": true,
-        "group": "gregcaporaso",
-        "name": "caporaso-lab-secrets",
-        "paths": [],
-        "rootPath": "$home/src/gregcaporaso/caporaso-lab-secrets"
-    },
-    {
-        "enabled": true,
-        "group": "gregcaporaso",
-        "name": "qiime2-meta-figures",
-        "paths": [],
-        "rootPath": "$home/src/gregcaporaso/qiime2-meta-figures"
-    },
-    {
-        "enabled": true,
-        "group": "",
-        "name": "dotfiles",
-        "paths": [],
-        "rootPath": "$home/.dotfiles"
-    }
-]

vscode/qiime2-1.code-workspace

@@ -0,0 +1,244 @@
+{
+    "folders": [
+        {
+            "name": "action-library-packaging",
+            "path": "/Users/matthew/projects/qiime2/action-library-packaging"
+        },
+        {
+            "name": "bioconda-recipes",
+            "path": "/Users/matthew/projects/qiime2/bioconda-recipes"
+        },
+        {
+            "name": "busywork",
+            "path": "/Users/matthew/projects/qiime2/busywork"
+        },
+        {
+            "name": "busywork2_action_playground",
+            "path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
+        },
+        {
+            "name": "caporaso-lab-secrets",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
+        },
+        {
+            "name": "caporaso-lab.github.io",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
+        },
+        {
+            "name": "data",
+            "path": "/Users/matthew/projects/qiime2/data"
+        },
+        {
+            "name": "data302",
+            "path": "/Users/matthew/projects/qiime2/data302"
+        },
+        {
+            "name": "deblur",
+            "path": "/Users/matthew/projects/qiime2/deblur"
+        },
+        {
+            "name": "dev-docs",
+            "path": "/Users/matthew/projects/qiime2/dev-docs"
+        },
+        {
+            "name": "discourse-unhandled-tagger",
+            "path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
+        },
+        {
+            "name": "docs",
+            "path": "/Users/matthew/projects/qiime2/docs"
+        },
+        {
+            "name": "dotfiles",
+            "path": "/Users/matthew/.dotfiles"
+        },
+        {
+            "name": "environment-files",
+            "path": "/Users/matthew/projects/qiime2/environment-files"
+        },
+        {
+            "name": "keemei",
+            "path": "/Users/matthew/projects/qiime2/Keemei"
+        },
+        {
+            "name": "library",
+            "path": "/Users/matthew/projects/qiime2/library"
+        },
+        {
+            "name": "logos",
+            "path": "/Users/matthew/projects/qiime2/logos"
+        },
+        {
+            "name": "paper2",
+            "path": "/Users/matthew/projects/qiime2/paper2"
+        },
+        {
+            "name": "pretrained-feature-classifiers",
+            "path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
+        },
+        {
+            "name": "q2-alignment",
+            "path": "/Users/matthew/projects/qiime2/q2-alignment"
+        },
+        {
+            "name": "q2-composition",
+            "path": "/Users/matthew/projects/qiime2/q2-composition"
+        },
+        {
+            "name": "q2-cutadapt",
+            "path": "/Users/matthew/projects/qiime2/q2-cutadapt"
+        },
+        {
+            "name": "q2-dada2",
+            "path": "/Users/matthew/projects/qiime2/q2-dada2"
+        },
+        {
+            "name": "q2-deblur",
+            "path": "/Users/matthew/projects/qiime2/q2-deblur"
+        },
+        {
+            "name": "q2-demux",
+            "path": "/Users/matthew/projects/qiime2/q2-demux"
+        },
+        {
+            "name": "q2-diversity",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity"
+        },
+        {
+            "name": "q2-diversity-lib",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
+        },
+        {
+            "name": "q2-emperor",
+            "path": "/Users/matthew/projects/qiime2/q2-emperor"
+        },
+        {
+            "name": "q2-feature-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
+        },
+        {
+            "name": "q2-feature-table",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-table"
+        },
+        {
+            "name": "q2-fragment-insertion",
+            "path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
+        },
+        {
+            "name": "q2-gneiss",
+            "path": "/Users/matthew/projects/qiime2/q2-gneiss"
+        },
+        {
+            "name": "q2-longitudinal",
+            "path": "/Users/matthew/projects/qiime2/q2-longitudinal"
+        },
+        {
+            "name": "q2-metadata",
+            "path": "/Users/matthew/projects/qiime2/q2-metadata"
+        },
+        {
+            "name": "q2-mystery-stew",
+            "path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
+        },
+        {
+            "name": "q2-no-op",
+            "path": "/Users/matthew/projects/qiime2/q2-no-op"
+        },
+        {
+            "name": "q2-phylogenomics",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
+        },
+        {
+            "name": "q2-phylogeny",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogeny"
+        },
+        {
+            "name": "q2-quality-control",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-control"
+        },
+        {
+            "name": "q2-quality-filter",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-filter"
+        },
+        {
+            "name": "q2-sample-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
+        },
+        {
+            "name": "q2-shogun",
+            "path": "/Users/matthew/projects/qiime2/q2-shogun"
+        },
+        {
+            "name": "q2-taxa",
+            "path": "/Users/matthew/projects/qiime2/q2-taxa"
+        },
+        {
+            "name": "q2-types",
+            "path": "/Users/matthew/projects/qiime2/q2-types"
+        },
+        {
+            "name": "q2-vsearch",
+            "path": "/Users/matthew/projects/qiime2/q2-vsearch"
+        },
+        {
+            "name": "q2cli",
+            "path": "/Users/matthew/projects/qiime2/q2cli"
+        },
+        {
+            "name": "q2cwl",
+            "path": "/Users/matthew/projects/qiime2/q2cwl"
+        },
+        {
+            "name": "q2galaxy",
+            "path": "/Users/matthew/projects/qiime2/q2galaxy"
+        },
+        {
+            "name": "q2studio",
+            "path": "/Users/matthew/projects/qiime2/q2studio"
+        },
+        {
+            "name": "q2templates",
+            "path": "/Users/matthew/projects/qiime2/q2templates"
+        },
+        {
+            "name": "q2view",
+            "path": "/Users/matthew/projects/qiime2/q2view"
+        },
+        {
+            "name": "qiime2",
+            "path": "/Users/matthew/projects/qiime2/qiime2"
+        },
+        {
+            "name": "qiime2-meta-figures",
+            "path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
+        },
+        {
+            "name": "qiime2.github.io",
+            "path": "/Users/matthew/projects/qiime2/qiime2.github.io"
+        },
+        {
+            "name": "scikit-bio",
+            "path": "/Users/matthew/projects/qiime2/scikit-bio"
+        },
+        {
+            "name": "template-repo",
+            "path": "/Users/matthew/projects/qiime2/template-repo"
+        },
+        {
+            "name": "view.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/view.qiime2.org"
+        },
+        {
+            "name": "vm-playbooks",
+            "path": "/Users/matthew/projects/qiime2/vm-playbooks"
+        },
+        {
+            "name": "workshop-playbooks",
+            "path": "/Users/matthew/projects/qiime2/workshop-playbooks"
+        },
+        {
+            "name": "workshops.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
+        }
+    ]
+}

vscode/qiime2-2.code-workspace

@@ -0,0 +1,244 @@
+{
+    "folders": [
+        {
+            "name": "action-library-packaging",
+            "path": "/Users/matthew/projects/qiime2/action-library-packaging"
+        },
+        {
+            "name": "bioconda-recipes",
+            "path": "/Users/matthew/projects/qiime2/bioconda-recipes"
+        },
+        {
+            "name": "busywork",
+            "path": "/Users/matthew/projects/qiime2/busywork"
+        },
+        {
+            "name": "busywork2_action_playground",
+            "path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
+        },
+        {
+            "name": "caporaso-lab-secrets",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
+        },
+        {
+            "name": "caporaso-lab.github.io",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
+        },
+        {
+            "name": "data",
+            "path": "/Users/matthew/projects/qiime2/data"
+        },
+        {
+            "name": "data302",
+            "path": "/Users/matthew/projects/qiime2/data302"
+        },
+        {
+            "name": "deblur",
+            "path": "/Users/matthew/projects/qiime2/deblur"
+        },
+        {
+            "name": "dev-docs",
+            "path": "/Users/matthew/projects/qiime2/dev-docs"
+        },
+        {
+            "name": "discourse-unhandled-tagger",
+            "path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
+        },
+        {
+            "name": "docs",
+            "path": "/Users/matthew/projects/qiime2/docs"
+        },
+        {
+            "name": "dotfiles",
+            "path": "/Users/matthew/.dotfiles"
+        },
+        {
+            "name": "environment-files",
+            "path": "/Users/matthew/projects/qiime2/environment-files"
+        },
+        {
+            "name": "keemei",
+            "path": "/Users/matthew/projects/qiime2/Keemei"
+        },
+        {
+            "name": "library",
+            "path": "/Users/matthew/projects/qiime2/library"
+        },
+        {
+            "name": "logos",
+            "path": "/Users/matthew/projects/qiime2/logos"
+        },
+        {
+            "name": "paper2",
+            "path": "/Users/matthew/projects/qiime2/paper2"
+        },
+        {
+            "name": "pretrained-feature-classifiers",
+            "path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
+        },
+        {
+            "name": "q2-alignment",
+            "path": "/Users/matthew/projects/qiime2/q2-alignment"
+        },
+        {
+            "name": "q2-composition",
+            "path": "/Users/matthew/projects/qiime2/q2-composition"
+        },
+        {
+            "name": "q2-cutadapt",
+            "path": "/Users/matthew/projects/qiime2/q2-cutadapt"
+        },
+        {
+            "name": "q2-dada2",
+            "path": "/Users/matthew/projects/qiime2/q2-dada2"
+        },
+        {
+            "name": "q2-deblur",
+            "path": "/Users/matthew/projects/qiime2/q2-deblur"
+        },
+        {
+            "name": "q2-demux",
+            "path": "/Users/matthew/projects/qiime2/q2-demux"
+        },
+        {
+            "name": "q2-diversity",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity"
+        },
+        {
+            "name": "q2-diversity-lib",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
+        },
+        {
+            "name": "q2-emperor",
+            "path": "/Users/matthew/projects/qiime2/q2-emperor"
+        },
+        {
+            "name": "q2-feature-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
+        },
+        {
+            "name": "q2-feature-table",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-table"
+        },
+        {
+            "name": "q2-fragment-insertion",
+            "path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
+        },
+        {
+            "name": "q2-gneiss",
+            "path": "/Users/matthew/projects/qiime2/q2-gneiss"
+        },
+        {
+            "name": "q2-longitudinal",
+            "path": "/Users/matthew/projects/qiime2/q2-longitudinal"
+        },
+        {
+            "name": "q2-metadata",
+            "path": "/Users/matthew/projects/qiime2/q2-metadata"
+        },
+        {
+            "name": "q2-mystery-stew",
+            "path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
+        },
+        {
+            "name": "q2-no-op",
+            "path": "/Users/matthew/projects/qiime2/q2-no-op"
+        },
+        {
+            "name": "q2-phylogenomics",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
+        },
+        {
+            "name": "q2-phylogeny",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogeny"
+        },
+        {
+            "name": "q2-quality-control",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-control"
+        },
+        {
+            "name": "q2-quality-filter",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-filter"
+        },
+        {
+            "name": "q2-sample-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
+        },
+        {
+            "name": "q2-shogun",
+            "path": "/Users/matthew/projects/qiime2/q2-shogun"
+        },
+        {
+            "name": "q2-taxa",
+            "path": "/Users/matthew/projects/qiime2/q2-taxa"
+        },
+        {
+            "name": "q2-types",
+            "path": "/Users/matthew/projects/qiime2/q2-types"
+        },
+        {
+            "name": "q2-vsearch",
+            "path": "/Users/matthew/projects/qiime2/q2-vsearch"
+        },
+        {
+            "name": "q2cli",
+            "path": "/Users/matthew/projects/qiime2/q2cli"
+        },
+        {
+            "name": "q2cwl",
+            "path": "/Users/matthew/projects/qiime2/q2cwl"
+        },
+        {
+            "name": "q2galaxy",
+            "path": "/Users/matthew/projects/qiime2/q2galaxy"
+        },
+        {
+            "name": "q2studio",
+            "path": "/Users/matthew/projects/qiime2/q2studio"
+        },
+        {
+            "name": "q2templates",
+            "path": "/Users/matthew/projects/qiime2/q2templates"
+        },
+        {
+            "name": "q2view",
+            "path": "/Users/matthew/projects/qiime2/q2view"
+        },
+        {
+            "name": "qiime2",
+            "path": "/Users/matthew/projects/qiime2/qiime2"
+        },
+        {
+            "name": "qiime2-meta-figures",
+            "path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
+        },
+        {
+            "name": "qiime2.github.io",
+            "path": "/Users/matthew/projects/qiime2/qiime2.github.io"
+        },
+        {
+            "name": "scikit-bio",
+            "path": "/Users/matthew/projects/qiime2/scikit-bio"
+        },
+        {
+            "name": "template-repo",
+            "path": "/Users/matthew/projects/qiime2/template-repo"
+        },
+        {
+            "name": "view.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/view.qiime2.org"
+        },
+        {
+            "name": "vm-playbooks",
+            "path": "/Users/matthew/projects/qiime2/vm-playbooks"
+        },
+        {
+            "name": "workshop-playbooks",
+            "path": "/Users/matthew/projects/qiime2/workshop-playbooks"
+        },
+        {
+            "name": "workshops.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
+        }
+    ]
+}

vscode/qiime2-3.code-workspace

@@ -0,0 +1,244 @@
+{
+    "folders": [
+        {
+            "name": "action-library-packaging",
+            "path": "/Users/matthew/projects/qiime2/action-library-packaging"
+        },
+        {
+            "name": "bioconda-recipes",
+            "path": "/Users/matthew/projects/qiime2/bioconda-recipes"
+        },
+        {
+            "name": "busywork",
+            "path": "/Users/matthew/projects/qiime2/busywork"
+        },
+        {
+            "name": "busywork2_action_playground",
+            "path": "/Users/matthew/projects/qiime2/busywork2_action_playground"
+        },
+        {
+            "name": "caporaso-lab-secrets",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab-secrets"
+        },
+        {
+            "name": "caporaso-lab.github.io",
+            "path": "/Users/matthew/projects/qiime2/caporaso-lab.github.io"
+        },
+        {
+            "name": "data",
+            "path": "/Users/matthew/projects/qiime2/data"
+        },
+        {
+            "name": "data302",
+            "path": "/Users/matthew/projects/qiime2/data302"
+        },
+        {
+            "name": "deblur",
+            "path": "/Users/matthew/projects/qiime2/deblur"
+        },
+        {
+            "name": "dev-docs",
+            "path": "/Users/matthew/projects/qiime2/dev-docs"
+        },
+        {
+            "name": "discourse-unhandled-tagger",
+            "path": "/Users/matthew/projects/qiime2/discourse-unhandled-tagger"
+        },
+        {
+            "name": "docs",
+            "path": "/Users/matthew/projects/qiime2/docs"
+        },
+        {
+            "name": "dotfiles",
+            "path": "/Users/matthew/.dotfiles"
+        },
+        {
+            "name": "environment-files",
+            "path": "/Users/matthew/projects/qiime2/environment-files"
+        },
+        {
+            "name": "keemei",
+            "path": "/Users/matthew/projects/qiime2/Keemei"
+        },
+        {
+            "name": "library",
+            "path": "/Users/matthew/projects/qiime2/library"
+        },
+        {
+            "name": "logos",
+            "path": "/Users/matthew/projects/qiime2/logos"
+        },
+        {
+            "name": "paper2",
+            "path": "/Users/matthew/projects/qiime2/paper2"
+        },
+        {
+            "name": "pretrained-feature-classifiers",
+            "path": "/Users/matthew/projects/qiime2/pretrained-feature-classifiers"
+        },
+        {
+            "name": "q2-alignment",
+            "path": "/Users/matthew/projects/qiime2/q2-alignment"
+        },
+        {
+            "name": "q2-composition",
+            "path": "/Users/matthew/projects/qiime2/q2-composition"
+        },
+        {
+            "name": "q2-cutadapt",
+            "path": "/Users/matthew/projects/qiime2/q2-cutadapt"
+        },
+        {
+            "name": "q2-dada2",
+            "path": "/Users/matthew/projects/qiime2/q2-dada2"
+        },
+        {
+            "name": "q2-deblur",
+            "path": "/Users/matthew/projects/qiime2/q2-deblur"
+        },
+        {
+            "name": "q2-demux",
+            "path": "/Users/matthew/projects/qiime2/q2-demux"
+        },
+        {
+            "name": "q2-diversity",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity"
+        },
+        {
+            "name": "q2-diversity-lib",
+            "path": "/Users/matthew/projects/qiime2/q2-diversity-lib"
+        },
+        {
+            "name": "q2-emperor",
+            "path": "/Users/matthew/projects/qiime2/q2-emperor"
+        },
+        {
+            "name": "q2-feature-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-classifier"
+        },
+        {
+            "name": "q2-feature-table",
+            "path": "/Users/matthew/projects/qiime2/q2-feature-table"
+        },
+        {
+            "name": "q2-fragment-insertion",
+            "path": "/Users/matthew/projects/qiime2/q2-fragment-insertion"
+        },
+        {
+            "name": "q2-gneiss",
+            "path": "/Users/matthew/projects/qiime2/q2-gneiss"
+        },
+        {
+            "name": "q2-longitudinal",
+            "path": "/Users/matthew/projects/qiime2/q2-longitudinal"
+        },
+        {
+            "name": "q2-metadata",
+            "path": "/Users/matthew/projects/qiime2/q2-metadata"
+        },
+        {
+            "name": "q2-mystery-stew",
+            "path": "/Users/matthew/projects/qiime2/q2-mystery-stew"
+        },
+        {
+            "name": "q2-no-op",
+            "path": "/Users/matthew/projects/qiime2/q2-no-op"
+        },
+        {
+            "name": "q2-phylogenomics",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogenomics"
+        },
+        {
+            "name": "q2-phylogeny",
+            "path": "/Users/matthew/projects/qiime2/q2-phylogeny"
+        },
+        {
+            "name": "q2-quality-control",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-control"
+        },
+        {
+            "name": "q2-quality-filter",
+            "path": "/Users/matthew/projects/qiime2/q2-quality-filter"
+        },
+        {
+            "name": "q2-sample-classifier",
+            "path": "/Users/matthew/projects/qiime2/q2-sample-classifier"
+        },
+        {
+            "name": "q2-shogun",
+            "path": "/Users/matthew/projects/qiime2/q2-shogun"
+        },
+        {
+            "name": "q2-taxa",
+            "path": "/Users/matthew/projects/qiime2/q2-taxa"
+        },
+        {
+            "name": "q2-types",
+            "path": "/Users/matthew/projects/qiime2/q2-types"
+        },
+        {
+            "name": "q2-vsearch",
+            "path": "/Users/matthew/projects/qiime2/q2-vsearch"
+        },
+        {
+            "name": "q2cli",
+            "path": "/Users/matthew/projects/qiime2/q2cli"
+        },
+        {
+            "name": "q2cwl",
+            "path": "/Users/matthew/projects/qiime2/q2cwl"
+        },
+        {
+            "name": "q2galaxy",
+            "path": "/Users/matthew/projects/qiime2/q2galaxy"
+        },
+        {
+            "name": "q2studio",
+            "path": "/Users/matthew/projects/qiime2/q2studio"
+        },
+        {
+            "name": "q2templates",
+            "path": "/Users/matthew/projects/qiime2/q2templates"
+        },
+        {
+            "name": "q2view",
+            "path": "/Users/matthew/projects/qiime2/q2view"
+        },
+        {
+            "name": "qiime2",
+            "path": "/Users/matthew/projects/qiime2/qiime2"
+        },
+        {
+            "name": "qiime2-meta-figures",
+            "path": "/Users/matthew/projects/qiime2/qiime2-meta-figures"
+        },
+        {
+            "name": "qiime2.github.io",
+            "path": "/Users/matthew/projects/qiime2/qiime2.github.io"
+        },
+        {
+            "name": "scikit-bio",
+            "path": "/Users/matthew/projects/qiime2/scikit-bio"
+        },
+        {
+            "name": "template-repo",
+            "path": "/Users/matthew/projects/qiime2/template-repo"
+        },
+        {
+            "name": "view.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/view.qiime2.org"
+        },
+        {
+            "name": "vm-playbooks",
+            "path": "/Users/matthew/projects/qiime2/vm-playbooks"
+        },
+        {
+            "name": "workshop-playbooks",
+            "path": "/Users/matthew/projects/qiime2/workshop-playbooks"
+        },
+        {
+            "name": "workshops.qiime2.org",
+            "path": "/Users/matthew/projects/qiime2/workshops.qiime2.org"
+        }
+    ]
+}

vscode/settings.json

@@ -6,9 +6,22 @@
     "telemetry.enableCrashReporter": false,
 
     "workbench.colorTheme": "Base16 Dark Ashes",
+    "workbench.sideBar.location": "right",
 
     "window.zoomLevel": 0,
-    "window.restoreFullscreen": true,
+    "window.restoreFullscreen": false,
 
-    "python.jediEnabled": false
+    "python.jediEnabled": false,
-}
+
+    "git.confirmSync": false,
+    "githubPullRequests.remotes": [
+        "origin",
+        "upstream",
+        "thermokarst",
+        "qiime2"
+    ],
+    "[elixir]": {
+       "editor.tabSize": 2,
+       "editor.formatOnSave": true,
+    },
+}

vscode/tasks.json

@@ -7,4 +7,4 @@
             "command": "make test"
         }
     ]
-}
+}

zsh/zshenv

@@ -20,8 +20,8 @@ fi
 # Editors
 #
 
-export EDITOR='code'
+export EDITOR='vim'
-export VISUAL='code'
+export VISUAL='vim'
 export PAGER='less'
 
 #
@@ -67,16 +67,10 @@ fi
 typeset -gU cdpath fpath mailpath path
 
 # Set the the list of directories that cd searches.
-cdpath=(
+# cdpath=(
-  # shortcuts to projects
+#   .
-  $HOME/src/biocore
+#   $cdpath
-  $HOME/src/caporaso-lab
+# )
-  $HOME/src/gregcaporaso
-  $HOME/src/qiime2
-  $HOME/src/thermokarst
-  .
-  $cdpath
-)
 
 # Set the list of directories that Zsh searches for programs.
 path=(
@@ -85,9 +79,8 @@ path=(
   # miniconda
   /opt/miniconda3/bin
 
-  # yarn
+  # npm
-  $HOME/.yarn/bin
+  $HOME/.npm-packages/bin
-  $HOME/.config/yarn/global/node_modules/.bin
 
   # misc apps
   /Applications/Postgres.app/Contents/Versions/12/bin/

zsh/zshrc

@@ -15,16 +15,11 @@ if [[ -s "/opt/miniconda3/etc/profile.d/conda.sh" ]]; then
 fi
 
 # shortcuts
-alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25"
-alias mongod="mongod --config /usr/local/etc/mongod.conf"
-alias venv="source venv/bin/activate"
-alias devenv="deactivate"
 alias q="conda activate q2dev"
 alias i="ipython3"
 
 BASE16_SHELL=$HOME/.config/base16-shell/
 [ -n "$PS1" ] && [ -s $BASE16_SHELL/profile_helper.sh ] && eval "$($BASE16_SHELL/profile_helper.sh)"
-[ -f $HOME/.fzf.zsh ] && source $HOME/.fzf.zsh
 
 # Backup shortcuts (borrowed parts from https://github.com/laurent22/rsync-time-backup
 function prune_backups() {
@@ -71,7 +66,4 @@ function back_things_up() {
     # TODO: once confident pruning is working well, add that in here
 }
 
-
+ eval "$(gh completion -s zsh)"
-export PATH="$HOME/.yarn/bin:$HOME/.config/yarn/global/node_modules/.bin:$PATH"
-
-[ -f ~/.fzf.zsh ] && source ~/.fzf.zsh