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Optimize disk space usage for planemo test #1378

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merged 6 commits into from
Jul 20, 2023
Merged

Optimize disk space usage for planemo test #1378

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d93e83b
do a shallow copy from the bare repo in .planemo
bernt-matthias Jul 17, 2023
311f675
improvements/fixes for --no_cache_galaxy
bernt-matthias Jul 17, 2023
7d1a79d
lint
bernt-matthias Jul 17, 2023
48f9e22
allow for banch names containing `/`
bernt-matthias Jul 17, 2023
fa121e6
revert changes to git clone function
bernt-matthias Jul 18, 2023
24089af
make file:// conditional on depth
bernt-matthias Jul 18, 2023
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9 changes: 6 additions & 3 deletions planemo/galaxy/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1230,9 +1230,12 @@ def _install_galaxy(ctx, galaxy_root, env, kwds):

def _install_galaxy_via_download(ctx, galaxy_root, env, kwds):
branch = _galaxy_branch(kwds)
source = _galaxy_source(kwds)
if source.startswith("https://github.com/"):
source = source[len("https://github.com/") :]
untar_to(
"https://codeload.github.com/galaxyproject/galaxy/tar.gz/" + branch,
tar_args=["-xvzf", "-", "galaxy-" + branch],
f"https://codeload.github.com/{source}/tar.gz/{branch}",
tar_args=["--strip-components", "1", "-xvzf", "-", "galaxy-" + branch.replace("/", "-")],
dest_dir=galaxy_root,
)
_install_with_command(ctx, galaxy_root, env, kwds)
Expand All @@ -1241,7 +1244,7 @@ def _install_galaxy_via_download(ctx, galaxy_root, env, kwds):
def _install_galaxy_via_git(ctx, galaxy_root, env, kwds):
gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
branch = _galaxy_branch(kwds)
command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch)
command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch, depth=1)
exit_code = shell(command, env=env)
if exit_code != 0:
raise Exception("Failed to clone Galaxy via git")
Expand Down
12 changes: 11 additions & 1 deletion planemo/git.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import os
import subprocess
import urllib.parse
from typing import (
Dict,
List,
Expand Down Expand Up @@ -87,7 +88,12 @@ def checkout(ctx, remote_repo, local_path, branch=None, remote="origin", from_br


def command_clone(
ctx: "PlanemoCliContext", src: str, dest: str, mirror: bool = False, branch: Optional[str] = None
ctx: "PlanemoCliContext",
src: str,
dest: str,
mirror: bool = False,
branch: Optional[str] = None,
depth: Optional[int] = None,
) -> List[str]:
"""Produce a command-line string to clone a repository.

Expand All @@ -98,6 +104,10 @@ def command_clone(
cmd.append("--mirror")
if branch is not None:
cmd.extend(["--branch", branch])
if depth is not None:
cmd.extend(["--depth", str(depth)])
if urllib.parse.urlparse(src).scheme == "":
src = f"file://{src}"
cmd.extend([src, dest])
return cmd

Expand Down