Merge branch 'master' of github.com:pepkit/geofetch

.travis.yml

@@ -1,6 +1,7 @@
 language: python
 python:
   - "2.7"
+  - "3.5"
   - "3.6"
 os:
   - linux
@@ -9,7 +10,7 @@ install:
   - pip install .
   - pip install -r requirements/requirements-dev.txt
   - pip install -r requirements/requirements-test.txt
-script: pytest
+script: pytest --cov=geofetch
 branches:
   only:
     - dev

docs/README.md

@@ -20,8 +20,8 @@ pip install geofetch
 
 Now, run it on the command line:
 
-```bash
+```console
 geofetch --help
 ```
 
-Next, check out the [usage](usage) reference, or for a detailed walkthrough, head on over to the [tutorial](tutorial).
+Next, check out the [usage](usage) reference, or for a detailed walkthrough, head on over to the [tutorial](tutorial).

docs/changelog.md

@@ -1,6 +1,4 @@
 # Changelog
 
-## geofetch v0.1 (unreleased)
-
-  - First semi-functional release.
-
+## geofetch v0.1 (2019-02-27)
+- First semi-functional release.

geofetch/__init__.py

@@ -0,0 +1,4 @@
+""" Package-level data """
+from .geofetch import *
+from ._version import __version__
+

geofetch/geofetch.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 __author__ = "Nathan Sheffield"
+__all__ = ["parse_accessions"]
 
 # Outline:
 # INPUT: A list of GSE ids, optionally including GSM ids to limit to.
@@ -23,7 +24,7 @@
 import re
 import subprocess
 import sys
-from utils import Accession
+from .utils import Accession
 
 
 # A set of hard-coded keys if you want to limit to just a few instead of taking

requirements/requirements-all.txt

@@ -1,6 +1,4 @@
 attmap>=0.1.8
 colorama>=0.3.9
-pandas>=0.20.2
 pyyaml>=3.12
 peppy>=0.19.1
-

requirements/requirements-dev.txt

@@ -1,2 +1,2 @@
-mock==2.0.0
-pytest==3.0.7
+mock>=2.0.0
+pytest==3.10.1

setup.py

@@ -5,33 +5,27 @@
 import sys
 
 PACKAGE = "geofetch"
+REQDIR = "requirements"
 
 # Additional keyword arguments for setup().
 extra = {}
 
-# Ordinary dependencies
-DEPENDENCIES = []
-with open("requirements/requirements-all.txt", "r") as reqs_file:
-    for line in reqs_file:
-        if not line.strip():
-            continue
-        #DEPENDENCIES.append(line.split("=")[0].rstrip("<>"))
-        DEPENDENCIES.append(line)
 
-# numexpr for pandas
-try:
-    import numexpr
-except ImportError:
-    # No numexpr is OK for pandas.
-    pass
-else:
-    # pandas 0.20.2 needs updated numexpr; the claim is 2.4.6, but that failed.
-    DEPENDENCIES.append("numexpr>=2.6.2")
+def read_reqs(reqs_name):
+    deps = []
+    with open(os.path.join(REQDIR, "requirements-{}.txt".format(reqs_name)), 'r') as f:
+        for l in f:
+            if not l.strip():
+                continue
+            #deps.append(l.split("=")[0].rstrip("<>"))
+            deps.append(l)
+    return deps
+
 
 # 2to3
 if sys.version_info >= (3, ):
     extra["use_2to3"] = True
-extra["install_requires"] = DEPENDENCIES
+extra["install_requires"] = read_reqs("all")
 
 
 # Additional files to include with package
@@ -68,7 +62,6 @@ def get_static(name, condition=None):
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
         "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.4",
         "Programming Language :: Python :: 3.5",
         "Programming Language :: Python :: 3.6",
         "Topic :: Scientific/Engineering :: Bio-Informatics"
@@ -85,5 +78,8 @@ def get_static(name, condition=None):
     package_data={PACKAGE: ['templates/*']},
     scripts=scripts,
     include_package_data=True,
+    test_suite="tests", 
+    tests_require=read_reqs("dev"),
+    setup_requires=(["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []), 
     **extra
 )

tests/test_geofetch.py

@@ -1,7 +1,9 @@
-from geofetch.geofetch import parse_accessions
+from geofetch import parse_accessions
+import pytest
 
 
+@pytest.mark.skip("Not implemented")
 def test_accessions():
 	parse_accessions("GSE12345", None)
-	assert(True)
+	assert True