Merge pull request #108 from cgat-developers/AC-setup

reverted back to old setup.py

.github/workflows/cgatapps_python.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.7", "3.8"]
 
     defaults:
       run:
@@ -29,7 +29,7 @@ jobs:
           key:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('conda/environments/cgat-apps.yml') }}
-      - uses: mamba-org/provision-with-micromamba@main
+      - uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
           python-version: ${{ matrix.python-version }}

cgat/version.py

@@ -1 +1 @@
-__version__ = "0.6.3"
+__version__ = "0.6.4"

setup.py

@@ -35,12 +35,16 @@
 ########################################################################
 ########################################################################
 # Import setuptools
-# Use existing setuptools, otherwise raise ImportError.
+# Use existing setuptools, otherwise try ez_setup.
 try:
     import setuptools
-except ImportError as error:
-    print(error.__class__.__name__ + ": " + error.message)
-
+except ImportError:
+    # try to get via ez_setup
+    # ez_setup did not work on all machines tested as
+    # it uses curl with https protocol, which is not
+    # enabled in ScientificLinux
+    import ez_setup
+    ez_setup.use_setuptools()
 
 from setuptools import setup, find_packages, Extension
 
@@ -135,6 +139,35 @@ def is_exe(fpath):
 install_requires = []
 dependency_links = []
 
+for requirement in (
+        l.strip() for l in open('requires.txt') if not l.startswith("#")):
+    match = REPO_REQUIREMENT.match(requirement)
+    if match:
+        assert which(match.group('vcs')) is not None, \
+            ("VCS '%(vcs)s' must be installed in order to "
+             "install %(link)s" % match.groupdict())
+        install_requires.append("%(package)s==%(version)s" % match.groupdict())
+        dependency_links.append(match.group('link'))
+        continue
+
+    if requirement.startswith("https"):
+        install_requires.append(requirement)
+        continue
+
+    match = HTTPS_REQUIREMENT.match(requirement)
+    if match:
+        install_requires.append("%(package)s>=%(version)s" % match.groupdict())
+        dependency_links.append(match.group('link'))
+        continue
+
+    install_requires.append(requirement)
+
+if major == 2:
+    install_requires.extend(['web.py>=0.37',
+                             'xlwt>=0.7.4',
+                             'matplotlib-venn>=0.5'])
+elif major == 3:
+    pass
 
 cgat_packages = find_packages()
 cgat_package_dirs = {'cgat': 'cgat'}