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maint: adding new rust project, gwar

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This commit is contained in:
Matthew Ryan Dillon 2021-06-30 20:05:19 -07:00
parent 85d491cf64
commit 82b970a105
4 changed files with 229 additions and 250 deletions
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5
README.md
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@ -1,6 +1,9 @@
# dotfiles # dotfiles
```bash ```bash
$ wget -O gwar https://github.com/thermokarst/gwar/releases/download/0.0.1/gwar-macos
$ chmod +x gwar
$ ./gwar ~/.dotfiles/repos.toml
$ git clone --origin pingo ssh://git@pingo.thermokar.st/dotfiles ~/.dotfiles $ git clone --origin pingo ssh://git@pingo.thermokar.st/dotfiles ~/.dotfiles
$ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell $ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell
$ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto" $ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto"
@ -38,8 +41,6 @@ $ sudo sh Miniconda3-latest-MacOSX-x86_64.sh -p /opt/miniconda3 -b
$ sudo conda update conda $ sudo conda update conda
$ wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml $ wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml
$ conda env create -n q2dev --file qiime2-latest-py38-osx-conda.yml $ conda env create -n q2dev --file qiime2-latest-py38-osx-conda.yml
$ conda create -n dotfiles -c conda-forge pygit2
$ conda run -n dotfiles python ~/.dotfiles/bin/sync_git_repos.py ~/.dotfiles/repos.ini
``` ```
## manual apps ## manual apps

76
bin/sync_git_repos.py
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@ -1,76 +0,0 @@
import configparser
import os
import sys
import pygit2
def init_repo(repo_name, repo_fp, remote, remote_name, callbacks,
github_peers):
repo = pygit2.discover_repository(repo_fp)
if repo is None:
print('cloning %s' % remote)
init_remote = lambda r, n, u: r.remotes.create(remote_name, u)
repo = pygit2.clone_repository(remote, repo_fp, remote=init_remote,
callbacks=callbacks)
else:
print('already cloned %s' % remote)
repo = pygit2.Repository(repo)
try:
repo.remotes[remote_name]
except:
repo.remotes.create(remote_name, remote)
for peer in github_peers:
url = 'ssh://git@github.com/%s/%s' % (peer, repo_name)
try:
repo.remotes[peer]
except KeyError:
repo.remotes.create(peer, url)
if repo.remotes[peer].url != url:
repo.remotes.set_url(peer, url)
def sync_workspace(workspace_fp, repos, remote_host, remote_name, callbacks,
github_peers):
if not os.path.exists(workspace_fp):
os.makedirs(workspace_fp)
for repo in repos:
repo_fp = os.path.join(workspace_fp, repo)
remote = 'ssh://%s/%s' % (remote_host, repo)
init_repo(repo, repo_fp, remote, remote_name, callbacks, github_peers)
if __name__ == '__main__':
ini_fp = sys.argv[1]
cfg = configparser.ConfigParser()
cfg.read(ini_fp)
pub_fp = os.path.expanduser('~/.ssh/id_ecdsa.pub')
priv_fp = os.path.expanduser('~/.ssh/id_ecdsa')
keypair = pygit2.Keypair('git', pub_fp, priv_fp, '')
callbacks = pygit2.RemoteCallbacks(credentials=keypair)
for section in cfg.sections():
workspace_fp = cfg[section]['workspace']
workspace_fp = os.path.expanduser(workspace_fp)
repos = cfg[section]['repos'].split(',')
repos = [r.strip() for r in repos]
if '' in repos:
repos.remove('')
remote_host = cfg[section]['remote_host']
remote_name = cfg[section]['remote_name']
github_peers = cfg[section]['github_peers'].split(',')
if '' in github_peers:
github_peers.remove('')
sync_workspace(workspace_fp, repos, remote_host,
remote_name, callbacks, github_peers)

172
repos.ini
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@ -1,172 +0,0 @@
[personal]
workspace=~/projects/personal
remote_host=git@pingo.thermokar.st
remote_name=pingo
github_peers=
repos=
akdillon,
aoc2020,
cs685,
dot_ssh,
dotfiles,
elixir-class,
gitolite-admin,
gpx-web-utils,
notes,
pingo,
planner,
thermokar.st,
zettel,
[personal-dokku]
workspace=~/projects/personal
remote_host=dokku@pingo.thermokar.st
remote_name=dokku
github_peers=
repos=
akdillon,
planner,
thermokar.st,
zettel,
[mds]
workspace=~/projects/mds
remote_host=git@pingo.thermokar.st
remote_name=pingo
github_peers=
repos=
arctic_hibernators_schema,
bactdb,
bactdb_data,
ccdb-api,
ccdb-old,
ccdb-web,
drf_ember_pagination,
hibernators,
hibernators-web,
hymenobacterdotinfo,
[github_thermokast_personal]
workspace=~/projects/personal
remote_host=git@github.com/thermokarst
remote_name=thermokarst
github_peers=
repos=
thermokarst,
[github_thermokarst_qiime2]
workspace=~/projects/qiime2
remote_host=git@github.com/thermokarst
remote_name=thermokarst
github_peers=
repos=
q2-no-op,
workflows-playground,
[github_thermokarst_forks_qiime2]
workspace=~/projects/qiime2
remote_host=git@github.com/qiime2
remote_name=qiime2
github_peers=ebolyen,gregcaporaso,ChrisKeefe,Oddant1,nbokulich,andrewsanchez,cherman2,thermokarst-forks,Keegan-Evans,lizgehret
repos=
Keemei,
action-library-packaging,
busywork,
conda-channel-resource,
data302,
dev-docs,
docs,
environment-files,
library,
logos,
paper1,
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-phylogeny,
q2-quality-control,
q2-quality-filter,
q2-sample-classifier,
q2-taxa,
q2-types,
q2-vsearch,
q2cli,
q2cwl,
q2galaxy,
q2lint,
q2studio,
q2templates,
q2view,
qiime2,
qiime2.github.io,
sphinx-ext-qiime2,
sphinx-qiime2-theme,
static-site-infrastructure,
template-repo,
view.qiime2.org,
vm-playbooks,
workshop-playbooks,
workshops,
[github_thermokarst_forks_caporaso_lab]
workspace=~/projects/qiime2
remote_host=git@github.com/caporaso-lab
remote_name=caporaso-lab
github_peers=ebolyen,gregcaporaso,thermokarst-forks
repos=
caporaso-lab.github.io,
code-of-conduct,
genome-sampler,
pretrained-feature-classifiers,
q2-phylogenomics,
[github_thermokarst_forks_biocore]
workspace=~/projects/qiime2
remote_host=git@github.com/biocore
remote_name=biocore
github_peers=ebolyen,thermokarst-forks
repos=
deblur,
emperor,
gneiss,
scikit-bio,
[github_thermokarst_forks_bokulich_lab]
workspace=~/projects/qiime2
remote_host=git@github.com/bokulich-lab
remote_name=bokulich-lab
github_peers=nbokulich,thermokarst-forks
repos=
RESCRIPt,
[github_thermokarst_forks_conda_forge]
workspace=~/projects/qiime2
remote_host=git@github.com/conda-forge
remote_name=conda-forge
github_peers=thermokarst-forks
repos=
biom-format-feedstock,
ijson-feedstock,
scikit-bio-feedstock,
[github_gregcaporaso]
workspace=~/projects/qiime2
remote_host=git@github.com/gregcaporaso
remote_name=gregcaporaso
github_peers=
repos=
caporaso-lab-secrets,

226
repos.toml Normal file
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@ -0,0 +1,226 @@
# personal
[[workspace]]
path = "$HOME/Desktop/projects/personal"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@pingo.thermokar.st"
origin.name = "pingo"
repos = [
"cs685",
"dot_ssh",
"dotfiles",
"elixir-class",
"gitolite-admin",
"gpx-web-utils",
"gwar",
"notes",
"pingo",
]
remotes = []
# personal-dokku
[[workspace]]
path = "$HOME/Desktop/projects/personal"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@pingo.thermokar.st"
origin.name = "pingo"
repos = [
"akdillon",
"planner",
"thermokar.st",
"zettel",
]
remotes = [
{ name = "dokku", base_addr = "ssh://dokku@pingo.thermokar.st" },
]
# mds
[[workspace]]
path = "$HOME/Desktop/projects/mds"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@pingo.thermokar.st"
origin.name = "pingo"
repos = [
"arctic_hibernators_schema",
"bactdb",
"bactdb_data",
"ccdb-api",
"ccdb-old",
"ccdb-web",
"drf_ember_pagination",
"hibernators",
"hibernators-web",
"hymenobacterdotinfo",
]
remotes = []
# github-thermokarst-personal
[[workspace]]
path = "$HOME/Desktop/projects/personal"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/thermokarst"
origin.name = "thermokarst"
repos = [
"thermokarst",
]
remotes = []
# github-thermokarst-qiime2
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/thermokarst"
origin.name = "thermokarst"
repos = [
"q2-no-op",
"workflows-playground",
]
remotes = []
# github-thermokarst-forks-qiime2
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/qiime2"
origin.name = "qiime2"
repos = [
"Keemei",
"action-library-packaging",
"busywork",
"conda-channel-resource",
"data302",
"dev-docs",
"docs",
"environment-files",
"library",
"logos",
"paper1",
"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-phylogeny",
"q2-quality-control",
"q2-quality-filter",
"q2-sample-classifier",
"q2-taxa",
"q2-types",
"q2-vsearch",
"q2cli",
"q2cwl",
"q2galaxy",
"q2lint",
"q2studio",
"q2templates",
"q2view",
"qiime2",
"qiime2.github.io",
"sphinx-ext-qiime2",
"sphinx-qiime2-theme",
"static-site-infrastructure",
"template-repo",
"view.qiime2.org",
"vm-playbooks",
"workshop-playbooks",
"workshops",
]
remotes = [
{ name = "ChrisKeefe", base_addr = "ssh://git@github.com/ChrisKeefe" },
{ name = "Keegan-Evans", base_addr = "ssh://git@github.com/Keegan-Evans" },
{ name = "Oddant1", base_addr = "ssh://git@github.com/Oddant1" },
{ name = "cherman2", base_addr = "ssh://git@github.com/cherman2" },
{ name = "ebolyen", base_addr = "ssh://git@github.com/ebolyen" },
{ name = "gregcaporaso", base_addr = "ssh://git@github.com/gregcaporaso" },
{ name = "lizgehret", base_addr = "ssh://git@github.com/lizgehret" },
{ name = "nbokulich", base_addr = "ssh://git@github.com/nbokulich" },
{ name = "thermokarst-forks", base_addr = "ssh://git@github.com/thermokarst-forks" },
]
# github-thermokarst-forks-caporaso-lab
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/caporaso-lab"
origin.name = "caporaso-lab"
repos = [
"caporaso-lab.github.io",
"code-of-conduct",
"genome-sampler",
"pretrained-feature-classifiers",
"q2-phylogenomics",
]
remotes = [
{ name = "ebolyen", base_addr = "ssh://git@github.com/ebolyen" },
{ name = "gregcaporaso", base_addr = "ssh://git@github.com/gregcaporaso" },
{ name = "thermokarst-forks", base_addr = "ssh://git@github.com/thermokarst-forks" },
]
# github-thermokarst-forks-biocore
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/biocore"
origin.name = "biocore"
repos = [
"deblur",
"emperor",
"gneiss",
"scikit-bio",
]
remotes = [
{ name = "ebolyen", base_addr = "ssh://git@github.com/ebolyen" },
{ name = "thermokarst-forks", base_addr = "ssh://git@github.com/thermokarst-forks" },
]
# github-thermokarst-forks-bokulich-lab
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/bokulich-lab"
origin.name = "bokulich-lab"
repos = [
"RESCRIPt",
]
remotes = [
{ name = "nbokulich", base_addr = "ssh://git@github.com/nbokulich" },
{ name = "thermokarst-forks", base_addr = "ssh://git@github.com/thermokarst-forks" },
]
# github-thermokarst-forks-conda-forge
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/conda-forge"
origin.name = "conda-forge"
repos = [
"biom-format-feedstock",
"ijson-feedstock",
"scikit-bio-feedstock",
]
remotes = [
{ name = "thermokarst-forks", base_addr = "ssh://git@github.com/thermokarst-forks" },
]
# github-gregcaporaso
[[workspace]]
path = "$HOME/Desktop/projects/qiime2"
ssh_key_path = "$HOME/.ssh/id_ecdsa"
origin.base_addr = "ssh://git@github.com/gregcaporaso"
origin.name = "gregcaporaso"
repos = [
"caporaso-lab-secrets",
"qiime2-meta-figures",
]
remotes = []