Changes to setup.py to facilitate making distributions from MacOS

Author: jrfaeder

bionetgen/assets/BNGVERSION

@@ -1 +1 @@
-BioNetGen-2.9.1
+BioNetGen-2.9.1

bionetgen/assets/ghapi.json

@@ -1 +1 @@
-{"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/113526748", "assets_url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/113526748/assets", "upload_url": "https://uploads.github.com/repos/RuleWorld/bionetgen/releases/113526748/assets{?name,label}", "html_url": "https://github.com/RuleWorld/bionetgen/releases/tag/BioNetGen-2.9.0", "id": 113526748, "author": {"login": "mr2cents", "id": 86616300, "node_id": "MDQ6VXNlcjg2NjE2MzAw", "avatar_url": "https://avatars.githubusercontent.com/u/86616300?v=4", "gravatar_id": "", "url": "https://api.github.com/users/mr2cents", "html_url": "https://github.com/mr2cents", "followers_url": "https://api.github.com/users/mr2cents/followers", "following_url": "https://api.github.com/users/mr2cents/following{/other_user}", "gists_url": "https://api.github.com/users/mr2cents/gists{/gist_id}", "starred_url": "https://api.github.com/users/mr2cents/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/mr2cents/subscriptions", "organizations_url": "https://api.github.com/users/mr2cents/orgs", "repos_url": "https://api.github.com/users/mr2cents/repos", "events_url": "https://api.github.com/users/mr2cents/events{/privacy}", "received_events_url": "https://api.github.com/users/mr2cents/received_events", "type": "User", "site_admin": false}, "node_id": "RE_kwDOAe1CjM4GxEfc", "tag_name": "BioNetGen-2.9.0", "target_commitish": "master", "name": "BioNetGen-2.9.0", "draft": false, "prerelease": false, "created_at": "2023-07-25T16:44:50Z", "published_at": "2023-07-25T17:03:16Z", "assets": [{"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/118587100", "id": 118587100, "node_id": "RA_kwDOAe1CjM4HEX7c", "name": "BioNetGen-2.9.0-linux.tar.gz", "label": null, "uploader": {"login": "mr2cents", "id": 86616300, "node_id": "MDQ6VXNlcjg2NjE2MzAw", "avatar_url": "https://avatars.githubusercontent.com/u/86616300?v=4", "gravatar_id": "", "url": "https://api.github.com/users/mr2cents", "html_url": "https://github.com/mr2cents", "followers_url": "https://api.github.com/users/mr2cents/followers", "following_url": "https://api.github.com/users/mr2cents/following{/other_user}", "gists_url": "https://api.github.com/users/mr2cents/gists{/gist_id}", "starred_url": "https://api.github.com/users/mr2cents/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/mr2cents/subscriptions", "organizations_url": "https://api.github.com/users/mr2cents/orgs", "repos_url": "https://api.github.com/users/mr2cents/repos", "events_url": "https://api.github.com/users/mr2cents/events{/privacy}", "received_events_url": "https://api.github.com/users/mr2cents/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 78233963, "download_count": 2, "created_at": "2023-07-25T17:01:54Z", "updated_at": "2023-07-25T17:02:00Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.0/BioNetGen-2.9.0-linux.tar.gz"}, {"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/118582570", "id": 118582570, "node_id": "RA_kwDOAe1CjM4HEW0q", "name": "BioNetGen-2.9.0-mac.tar.gz", "label": null, "uploader": {"login": "mr2cents", "id": 86616300, "node_id": "MDQ6VXNlcjg2NjE2MzAw", "avatar_url": "https://avatars.githubusercontent.com/u/86616300?v=4", "gravatar_id": "", "url": "https://api.github.com/users/mr2cents", "html_url": "https://github.com/mr2cents", "followers_url": "https://api.github.com/users/mr2cents/followers", "following_url": "https://api.github.com/users/mr2cents/following{/other_user}", "gists_url": "https://api.github.com/users/mr2cents/gists{/gist_id}", "starred_url": "https://api.github.com/users/mr2cents/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/mr2cents/subscriptions", "organizations_url": "https://api.github.com/users/mr2cents/orgs", "repos_url": "https://api.github.com/users/mr2cents/repos", "events_url": "https://api.github.com/users/mr2cents/events{/privacy}", "received_events_url": "https://api.github.com/users/mr2cents/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 48595935, "download_count": 0, "created_at": "2023-07-25T16:39:00Z", "updated_at": "2023-07-25T16:39:05Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.0/BioNetGen-2.9.0-mac.tar.gz"}, {"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/118582606", "id": 118582606, "node_id": "RA_kwDOAe1CjM4HEW1O", "name": "BioNetGen-2.9.0-win.tar.gz", "label": null, "uploader": {"login": "mr2cents", "id": 86616300, "node_id": "MDQ6VXNlcjg2NjE2MzAw", "avatar_url": "https://avatars.githubusercontent.com/u/86616300?v=4", "gravatar_id": "", "url": "https://api.github.com/users/mr2cents", "html_url": "https://github.com/mr2cents", "followers_url": "https://api.github.com/users/mr2cents/followers", "following_url": "https://api.github.com/users/mr2cents/following{/other_user}", "gists_url": "https://api.github.com/users/mr2cents/gists{/gist_id}", "starred_url": "https://api.github.com/users/mr2cents/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/mr2cents/subscriptions", "organizations_url": "https://api.github.com/users/mr2cents/orgs", "repos_url": "https://api.github.com/users/mr2cents/repos", "events_url": "https://api.github.com/users/mr2cents/events{/privacy}", "received_events_url": "https://api.github.com/users/mr2cents/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 42114907, "download_count": 1, "created_at": "2023-07-25T16:39:16Z", "updated_at": "2023-07-25T16:39:20Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.0/BioNetGen-2.9.0-win.tar.gz"}], "tarball_url": "https://api.github.com/repos/RuleWorld/bionetgen/tarball/BioNetGen-2.9.0", "zipball_url": "https://api.github.com/repos/RuleWorld/bionetgen/zipball/BioNetGen-2.9.0", "body": "### Major changes\r\n* Species are exported to a SBML initial assignments block. Constant expressions are also exported in initial assignments block as long as they weren't a part of the original species block. This will improve the functionality of the exported SBML output for downstream tools.\r\n\r\n### Minor changes\r\n* Referring to observables or functions within species will result in an error as it could lead to circular dependency."}
+{"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/143539756", "assets_url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/143539756/assets", "upload_url": "https://uploads.github.com/repos/RuleWorld/bionetgen/releases/143539756/assets{?name,label}", "html_url": "https://github.com/RuleWorld/bionetgen/releases/tag/BioNetGen-2.9.1", "id": 143539756, "author": {"login": "jrfaeder", "id": 8277248, "node_id": "MDQ6VXNlcjgyNzcyNDg=", "avatar_url": "https://avatars.githubusercontent.com/u/8277248?v=4", "gravatar_id": "", "url": "https://api.github.com/users/jrfaeder", "html_url": "https://github.com/jrfaeder", "followers_url": "https://api.github.com/users/jrfaeder/followers", "following_url": "https://api.github.com/users/jrfaeder/following{/other_user}", "gists_url": "https://api.github.com/users/jrfaeder/gists{/gist_id}", "starred_url": "https://api.github.com/users/jrfaeder/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/jrfaeder/subscriptions", "organizations_url": "https://api.github.com/users/jrfaeder/orgs", "repos_url": "https://api.github.com/users/jrfaeder/repos", "events_url": "https://api.github.com/users/jrfaeder/events{/privacy}", "received_events_url": "https://api.github.com/users/jrfaeder/received_events", "type": "User", "site_admin": false}, "node_id": "RE_kwDOAe1CjM4Ijj4s", "tag_name": "BioNetGen-2.9.1", "target_commitish": "master", "name": "BioNetGen-2.9.1", "draft": false, "prerelease": false, "created_at": "2024-02-25T22:15:48Z", "published_at": "2024-02-26T15:19:58Z", "assets": [{"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/153825093", "id": 153825093, "node_id": "RA_kwDOAe1CjM4JKy9F", "name": "BioNetGen-2.9.1-linux.tar.gz", "label": null, "uploader": {"login": "jrfaeder", "id": 8277248, "node_id": "MDQ6VXNlcjgyNzcyNDg=", "avatar_url": "https://avatars.githubusercontent.com/u/8277248?v=4", "gravatar_id": "", "url": "https://api.github.com/users/jrfaeder", "html_url": "https://github.com/jrfaeder", "followers_url": "https://api.github.com/users/jrfaeder/followers", "following_url": "https://api.github.com/users/jrfaeder/following{/other_user}", "gists_url": "https://api.github.com/users/jrfaeder/gists{/gist_id}", "starred_url": "https://api.github.com/users/jrfaeder/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/jrfaeder/subscriptions", "organizations_url": "https://api.github.com/users/jrfaeder/orgs", "repos_url": "https://api.github.com/users/jrfaeder/repos", "events_url": "https://api.github.com/users/jrfaeder/events{/privacy}", "received_events_url": "https://api.github.com/users/jrfaeder/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 10002325, "download_count": 0, "created_at": "2024-02-27T14:51:05Z", "updated_at": "2024-02-27T14:51:06Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.1/BioNetGen-2.9.1-linux.tar.gz"}, {"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/153825089", "id": 153825089, "node_id": "RA_kwDOAe1CjM4JKy9B", "name": "BioNetGen-2.9.1-mac.tar.gz", "label": null, "uploader": {"login": "jrfaeder", "id": 8277248, "node_id": "MDQ6VXNlcjgyNzcyNDg=", "avatar_url": "https://avatars.githubusercontent.com/u/8277248?v=4", "gravatar_id": "", "url": "https://api.github.com/users/jrfaeder", "html_url": "https://github.com/jrfaeder", "followers_url": "https://api.github.com/users/jrfaeder/followers", "following_url": "https://api.github.com/users/jrfaeder/following{/other_user}", "gists_url": "https://api.github.com/users/jrfaeder/gists{/gist_id}", "starred_url": "https://api.github.com/users/jrfaeder/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/jrfaeder/subscriptions", "organizations_url": "https://api.github.com/users/jrfaeder/orgs", "repos_url": "https://api.github.com/users/jrfaeder/repos", "events_url": "https://api.github.com/users/jrfaeder/events{/privacy}", "received_events_url": "https://api.github.com/users/jrfaeder/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 9118082, "download_count": 0, "created_at": "2024-02-27T14:51:04Z", "updated_at": "2024-02-27T14:51:05Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.1/BioNetGen-2.9.1-mac.tar.gz"}, {"url": "https://api.github.com/repos/RuleWorld/bionetgen/releases/assets/153825082", "id": 153825082, "node_id": "RA_kwDOAe1CjM4JKy86", "name": "BioNetGen-2.9.1-win.tar.gz", "label": null, "uploader": {"login": "jrfaeder", "id": 8277248, "node_id": "MDQ6VXNlcjgyNzcyNDg=", "avatar_url": "https://avatars.githubusercontent.com/u/8277248?v=4", "gravatar_id": "", "url": "https://api.github.com/users/jrfaeder", "html_url": "https://github.com/jrfaeder", "followers_url": "https://api.github.com/users/jrfaeder/followers", "following_url": "https://api.github.com/users/jrfaeder/following{/other_user}", "gists_url": "https://api.github.com/users/jrfaeder/gists{/gist_id}", "starred_url": "https://api.github.com/users/jrfaeder/starred{/owner}{/repo}", "subscriptions_url": "https://api.github.com/users/jrfaeder/subscriptions", "organizations_url": "https://api.github.com/users/jrfaeder/orgs", "repos_url": "https://api.github.com/users/jrfaeder/repos", "events_url": "https://api.github.com/users/jrfaeder/events{/privacy}", "received_events_url": "https://api.github.com/users/jrfaeder/received_events", "type": "User", "site_admin": false}, "content_type": "application/x-gzip", "state": "uploaded", "size": 22154721, "download_count": 0, "created_at": "2024-02-27T14:51:03Z", "updated_at": "2024-02-27T14:51:04Z", "browser_download_url": "https://github.com/RuleWorld/bionetgen/releases/download/BioNetGen-2.9.1/BioNetGen-2.9.1-win.tar.gz"}], "tarball_url": "https://api.github.com/repos/RuleWorld/bionetgen/tarball/BioNetGen-2.9.1", "zipball_url": "https://api.github.com/repos/RuleWorld/bionetgen/zipball/BioNetGen-2.9.1", "body": "Fixes a bug that led to invalid SBML files being produced when there were internal variables in a BNGL models. These are produced when anything other than a simple parameter name is used in a RateLaw associated with a rule.\r\n\r\n*NOTE:* These bundles do not include binaries for sbmlTranslator or library files for compiling and linking to the CVODE library. These files are included in previous release bundles if you need them. For import and atomization of SBML models we strongly suggest you use the Atomizer library and tools included in the latest release of PyBioNetGen. Its functionality and reliability is much greater than that of the old sbmlTranslator code.\r\n\r\n**Full Changelog**: https://github.com/RuleWorld/bionetgen/compare/BioNetGen-2.9.0...BioNetGen-2.9.1"}

setup.py

@@ -1,5 +1,16 @@
 from setuptools import setup, find_packages
 import sys, os, json, urllib, subprocess
+import shutil, tarfile, zipfile
+
+# Utility function for Mac idiosyncracy
+def get_folder (arch):
+    for fname in arch.getnames():
+        if (fname.startswith('._')):
+            continue
+        else:
+            break
+    print(fname)
+    return(fname)
 
 subprocess.check_call([sys.executable, "-m", "pip", "install", "numpy"])
 import urllib.request
@@ -22,7 +33,7 @@
 bng_version_tag = rls_json["tag_name"]
 with open("bionetgen/assets/BNGVERSION", "w") as f:
     f.write(bng_version_tag)
-# get assests
+# get assets
 assets = rls_json["assets"]
 for asset in assets:
     browser_url = asset["browser_download_url"]
@@ -36,7 +47,6 @@
         windows_url = browser_url
 
 # next download and place the appropriate files
-import os, shutil, tarfile, zipfile
 
 bng_downloaded = False
 for iurl, bng_url in enumerate([linux_url, mac_url, windows_url]):
@@ -72,13 +82,17 @@
     ext = bng_url.split(".")[-1]
     fname = "bng.{}".format(ext)
     # download bng distro
+    print(bng_url, fname)
     urllib.request.urlretrieve(bng_url, fname)
     # file extension dependent actions, tar for
     # mac and linux, zip for windows
     if iurl < 2:
         # if "tgz" == ext or "gz" == etx:
         bng_arch = tarfile.open(fname)
-        fold_name = bng_arch.getnames()[0]
+        # Find containing folder of the archive.
+        # On macs may need to skip first item because
+        # filesystem makes shadow files with `._` prepended.
+        fold_name = get_folder(bng_arch)
         bng_arch.extractall()
         # make sure bionetgen/bng exists
         if iurl == 0:
@@ -114,7 +128,7 @@
         # fold_name = bng_arch.namelist()[0]
         # bng_arch.extractall()
         bng_arch = tarfile.open(fname)
-        fold_name = bng_arch.getnames()[0]
+        fold_name = get_folder(bng_arch)
         bng_arch.extractall()
         # bng folder
         if iurl == 2:

test_tarfile.ipynb

@@ -0,0 +1,66 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import tarfile"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "BioNetGen-2.9.1\n"
+     ]
+    }
+   ],
+   "source": [
+    "fname=\"bng.gz\"\n",
+    "bng_arch = tarfile.open(fname)\n",
+    "for i in range(2):\n",
+    "    fold_name = bng_arch.getnames()[i]\n",
+    "    if (fold_name.startswith('._')):\n",
+    "        continue\n",
+    "    else:\n",
+    "        break\n",
+    "print(fold_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}