-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #5 from sys-bio/enable-azure-build
Enable builds on azure.
- Loading branch information
Showing
32 changed files
with
1,775 additions
and
837 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| """ | ||
| Get check from url. | ||
| Usage: | ||
| python getCheck.py <check_download_link> <check_install_prefix? | ||
| For example: | ||
| python getcheck.py https://github.com/sys-bio/check-13.x/releases/download/checkorg-13.0.0/check13-ubuntu-gcc10-rel.tar.gz /mnt/d/roadrunner/roadrunner/check-download-test/ubuntu | ||
| """ | ||
|
|
||
|
|
||
| import glob | ||
| import argparse | ||
| import os | ||
| from os.path import join, splitext, isdir, isfile | ||
| import zipfile | ||
| import tarfile | ||
| import requests | ||
| import io | ||
| import shutil | ||
|
|
||
| # command line arguments | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("check_download_link", type=str, help="Url to compressed check link to download") | ||
| parser.add_argument("check_install_prefix", type=str, help="Where to install check (directory that will contain bin, include, lib etc") | ||
| args = parser.parse_args() | ||
|
|
||
| # filename of downloaded zip, check-[debug|release].zip | ||
| compressed_check_filename = args.check_download_link.split('/')[-1] | ||
|
|
||
| # absolute path to compressed_check_filename | ||
| abs_compressed_check_filename = join(args.check_install_prefix, compressed_check_filename) | ||
|
|
||
| # e.g. ('check--[debug|release]', '.zip') | ||
| downloaded_check_folder, ext = splitext(compressed_check_filename) | ||
| # when link is tar.gz, get rid of extra .tar | ||
| if ".tar" in downloaded_check_folder: | ||
| downloaded_check_folder = downloaded_check_folder.replace(".tar", "") | ||
|
|
||
| # make install prefix if not exists | ||
| if not isdir(args.check_install_prefix): | ||
| os.makedirs(args.check_install_prefix) | ||
|
|
||
| print("compressed_check_filename".ljust(20), compressed_check_filename) | ||
| print("abs_compressed_check_filename".ljust(20), abs_compressed_check_filename) | ||
| print("downloaded_check_folder".ljust(20), downloaded_check_folder) | ||
| print("args.check_download_link".ljust(20), args.check_download_link) | ||
| print("downloaded_check_folder, ext".ljust(20), downloaded_check_folder, ext) | ||
|
|
||
| # we expect a folder called bin in | ||
| abs_downloaded_check_folder = join(args.check_install_prefix, downloaded_check_folder) | ||
|
|
||
| # Don't download if we already have it | ||
| if not isdir(join(abs_downloaded_check_folder, "bin")): | ||
| print("downloading check from {}".format(args.check_download_link)) | ||
| r = requests.get(args.check_download_link, stream=True) | ||
| if ext == ".zip": | ||
| z = zipfile.ZipFile(io.BytesIO(r.content)) | ||
| z.extractall(args.check_install_prefix) | ||
| elif ext == ".gz": | ||
| z = tarfile.open(fileobj=r.raw, mode="r|gz") | ||
| z.extractall(args.check_install_prefix) | ||
| else: | ||
| raise ValueError("Unsupported extension") | ||
| else : | ||
| print("Found existing check, not downloading check") | ||
|
|
||
| # move from unzip dir to check_install_prefix | ||
| folders = glob.glob(join(abs_downloaded_check_folder, "*")) | ||
| print(folders) | ||
| for f in folders: | ||
| shutil.move(f, args.check_install_prefix) | ||
|
|
||
|
|
||
| if isfile(abs_compressed_check_filename): | ||
| os.remove(abs_compressed_check_filename) | ||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| """ | ||
| Finds and renames the local phraSED-ML wheel file to work with any Python version. | ||
| Usage: | ||
| python renameWheel.py | ||
| For example: | ||
| python renameWheel.py | ||
| """ | ||
|
|
||
|
|
||
| from os import walk, rename | ||
|
|
||
| wfiles = [] | ||
| for __, _, files in walk("."): | ||
| wfiles += files | ||
|
|
||
| for file in wfiles: | ||
| if ".whl" not in file: | ||
| continue | ||
| fvec = file.split("-") | ||
| fvec[2] = "py3" | ||
| fvec[3] = "none" | ||
| if "linux_" in fvec[4]: | ||
| fvec[4] = fvec[4].replace("linux_", "manylinux2014_") | ||
| newname = "" | ||
| for fpart in fvec: | ||
| newname += "-" + fpart | ||
| newname = newname[1:] | ||
| rename(file, newname) | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.