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annotate env/lib/python3.7/site-packages/planemo/commands/cmd_clone.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """Module describing the planemo ``recipe_init`` command."""
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2 import click
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3
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4 from planemo import github_util
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5 from planemo import options
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6 from planemo.cli import command_function
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7 from planemo.config import planemo_option
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8
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9
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10 CLONE_GITHUB_TARGETS = {
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11 "tools-iuc": "galaxyproject/tools-iuc",
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12 "tools-devteam": "galaxyproject/tools-devteam",
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13 "galaxy": "galaxyproject/galaxy",
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14 "planemo": "galaxyproject/planemo",
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15 "tools-galaxyp": "galaxyproteomics/tools-galaxyp",
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16 "bioconda-recipes": "bioconda/bioconda-recipes",
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17 "homebrew-science": "Homebrew/homebrew-science",
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18 "workflows": "common-workflow-language/workflows",
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19 }
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20
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21
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22 def clone_target_arg():
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23 """Represent target to clone/branch."""
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24 return click.argument(
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25 "target",
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26 metavar="TARGET",
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27 type=click.STRING,
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28 )
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29
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30
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31 @click.command('clone')
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32 @planemo_option(
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33 "--fork/--skip_fork",
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34 default=True,
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35 is_flag=True,
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36 )
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37 @planemo_option(
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38 "--branch",
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39 type=click.STRING,
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40 default=None,
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41 help="Create a named branch on result."
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42 )
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43 @clone_target_arg()
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44 @options.optional_project_arg(exists=None, default="__NONE__")
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45 @command_function
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46 def cli(ctx, target, path, **kwds):
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47 """Short-cut to quickly clone, fork, and branch a relevant Github repo.
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48
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49 For instance, the following will clone, fork, and branch the tools-iuc
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50 repository to allow a subsequent pull request to fix a problem with bwa.
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51
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52
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53 \b
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54 $ planemo clone --branch bwa-fix tools-iuc
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55 $ cd tools-iuc
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56 $ # Make changes.
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57 $ git add -p # Add desired changes.
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58 $ git commit -m "Fix bwa problem."
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59 $ planemo pull_request -m "Fix bwa problem."
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60
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61 These changes do require that a github username and password are
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62 specified in ~/.planemo.yml.
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63 """
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64 if target in CLONE_GITHUB_TARGETS:
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65 target = "https://github.com/%s" % CLONE_GITHUB_TARGETS[target]
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66 # Pretty hacky that this path isn't treated as None.
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67 if path is None or path.endswith("__NONE__"):
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68 path = target.split("/")[-1]
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69 github_util.clone_fork_branch(ctx, target, path, **kwds)