From 51a3d8917f9e6cae4c8a4d659c477dc21af85ab3 Mon Sep 17 00:00:00 2001
From: Acribbs <a.p.cribbs@gmail.com>
Date: Mon, 26 Jul 2021 09:45:54 +0100
Subject: [PATCH 1/4] reverted back to old setup.py

---
 setup.py | 41 +++++++++++++++++++++++++++++++++++++----
 1 file changed, 37 insertions(+), 4 deletions(-)

diff --git a/setup.py b/setup.py
index 8171a5ad..adb4ccd7 100644
--- a/setup.py
+++ b/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'}

From 30a146ff1fb4a1e249ffb7f25887611d2b24e223 Mon Sep 17 00:00:00 2001
From: Acribbs <a.p.cribbs@gmail.com>
Date: Mon, 26 Jul 2021 09:48:06 +0100
Subject: [PATCH 2/4] revert back to miniconda github actions

---
 .github/workflows/cgatapps_python.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cgatapps_python.yml b/.github/workflows/cgatapps_python.yml
index d484cdd2..1d666e31 100644
--- a/.github/workflows/cgatapps_python.yml
+++ b/.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 }}

From 122943bd094222061d6c2a7413266bd136d585c4 Mon Sep 17 00:00:00 2001
From: Acribbs <a.p.cribbs@gmail.com>
Date: Mon, 26 Jul 2021 09:50:30 +0100
Subject: [PATCH 3/4] added requires.txt

---
 requires.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 requires.txt

diff --git a/requires.txt b/requires.txt
new file mode 100644
index 00000000..e69de29b

From 32a039f855988822232422e7deb611c8e63ac530 Mon Sep 17 00:00:00 2001
From: Acribbs <a.p.cribbs@gmail.com>
Date: Mon, 26 Jul 2021 10:06:40 +0100
Subject: [PATCH 4/4] update version

---
 cgat/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cgat/version.py b/cgat/version.py
index 63af8876..364e7bae 100644
--- a/cgat/version.py
+++ b/cgat/version.py
@@ -1 +1 @@
-__version__ = "0.6.3"
+__version__ = "0.6.4"