refactor: simplify dependency information (#704)

.github/ISSUE_TEMPLATE.md

@@ -8,8 +8,7 @@ Please explain:
 
 #### Code Sample
 
-Create a [minimal, complete, verifiable example
-](https://stackoverflow.com/help/mcve).
+Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
 
 ```python
 # Paste your code here.
@@ -20,9 +19,13 @@ Create a [minimal, complete, verifiable example
 
 #### Expected Output
 
-#### Output of `cobra.show_versions()`
+#### Dependency Information
+
+Please paste the output of `python -c "from cobra import show_versions;
+show_versions()"` in the details block below.
 
 <details>
-# Paste the output of `import cobra;cobra.show_versions()` here.
+
+[Paste output here.]
 
 </details>

cobra/__init__.py

@@ -11,7 +11,7 @@
 from cobra import flux_analysis, io
 from cobra.core import (
     DictList, Gene, Metabolite, Model, Object, Reaction, Species)
-from cobra.util.version_info import show_versions
+from cobra.util import show_versions
 
 __version__ = "0.11.3"
 

cobra/test/test_util.py

@@ -8,9 +8,7 @@
 import pytest
 from six.moves import range
 
-from cobra import DictList, Object
-from cobra.util.version_info import (
-    get_sys_info, get_pkg_info, show_versions, SYS_ORDER, PKG_ORDER)
+from cobra import DictList, Object, show_versions
 
 
 @pytest.fixture(scope="function")
@@ -297,56 +295,15 @@ def test_union(self, dict_list):
         assert test_list.index("test2") == 1
 
 
-class TestVersionInfo:
-    SKIP_OPTIONAL = frozenset([
-        "cobra", "python-libsbml", "lxml", "matplotlib", "palettable", "scipy",
-        "pymatbridge"])
+def test_show_versions(capsys):
+    show_versions()
+    captured = capsys.readouterr()
+    lines = captured.out.split("\n")
+    assert lines[1].startswith("System Information")
+    assert lines[2].startswith("==================")
+    assert lines[3].startswith("OS")
+    assert lines[4].startswith("OS-release")
+    assert lines[5].startswith("Python")
 
-    @pytest.fixture(scope="module")
-    def sys_info(self):
-        return get_sys_info()
-
-    @pytest.fixture(scope="module")
-    def pkg_info(self):
-        return get_pkg_info()
-
-    @pytest.mark.parametrize("key", SYS_ORDER)
-    def test_sys_info_key(self, key, sys_info):
-        assert key in sys_info
-
-    @pytest.mark.parametrize("key", SYS_ORDER)
-    def test_sys_info_value(self, key, sys_info):
-        assert len(sys_info[key]) > 0
-
-    @pytest.mark.parametrize("key", PKG_ORDER)
-    def test_pkg_info_key(self, key, pkg_info):
-        if key in self.SKIP_OPTIONAL:
-            pytest.skip()
-        assert key in pkg_info
-
-    @pytest.mark.parametrize("key", PKG_ORDER)
-    def test_pkg_info_value(self, key, pkg_info):
-        if key in self.SKIP_OPTIONAL:
-            pytest.skip()
-        assert len(pkg_info[key]) > 0
-
-    def test_show_versions(self, sys_info, pkg_info, capsys):
-        show_versions()
-        out, err = capsys.readouterr()
-        lines = out.split("\n")
-        i = 3
-        for key in SYS_ORDER:
-            line = lines[i]
-            assert line.startswith(key)
-            assert line.endswith(sys_info[key])
-            i += 1
-        i += 3
-        for key in PKG_ORDER:
-            line = lines[i]
-            if key in self.SKIP_OPTIONAL:
-                if line.startswith(key):
-                    i += 1
-                continue
-            assert line.startswith(key)
-            assert line.endswith(pkg_info[key])
-            i += 1
+    assert lines[7].startswith("Package Versions")
+    assert lines[8].startswith("================")

cobra/util/util.py

@@ -2,6 +2,8 @@
 
 from __future__ import absolute_import
 
+from depinfo import print_dependencies
+
 
 def format_long_string(string, max_length=50):
     if len(string) > max_length:
@@ -20,3 +22,8 @@ def __getitem__(self, item):
         except KeyError:
             value = self[item] = type(self)()
             return value
+
+
+def show_versions():
+    """Print dependency information."""
+    print_dependencies("cobra")

setup.py

@@ -47,7 +47,8 @@
         "numpy>=1.13",
         "pandas>=0.17.0",
         "optlang>=1.2.5",
-        "tabulate"
+        "tabulate",
+        "depinfo"
     ],
     tests_require=[
         "jsonschema > 2.5",