From d69ff80573a257a75ac2ffd0e738ea78834d9dca Mon Sep 17 00:00:00 2001
From: Simon Li <spli@dundee.ac.uk>
Date: Tue, 22 Sep 2020 14:12:32 +0100
Subject: [PATCH 1/3] Use pinned versions for all direct OMERO deps

---
 requirements-debian9.txt    |  1 +
 requirements-default.txt    |  1 +
 requirements-pinned.txt     | 16 ++++++++++++++++
 requirements-ubuntu1604.txt |  1 +
 setup.py                    | 35 +++++++++++++++++++++++------------
 5 files changed, 42 insertions(+), 12 deletions(-)
 create mode 100644 requirements-debian9.txt
 create mode 100644 requirements-default.txt
 create mode 100644 requirements-pinned.txt
 create mode 100644 requirements-ubuntu1604.txt

diff --git a/requirements-debian9.txt b/requirements-debian9.txt
new file mode 100644
index 0000000..a6adc2a
--- /dev/null
+++ b/requirements-debian9.txt
@@ -0,0 +1 @@
+tables==3.5.2
diff --git a/requirements-default.txt b/requirements-default.txt
new file mode 100644
index 0000000..368a7c7
--- /dev/null
+++ b/requirements-default.txt
@@ -0,0 +1 @@
+tables==3.6.1
diff --git a/requirements-pinned.txt b/requirements-pinned.txt
new file mode 100644
index 0000000..6a41c4a
--- /dev/null
+++ b/requirements-pinned.txt
@@ -0,0 +1,16 @@
+omero-py==5.8.0
+
+# https://github.com/ome/omero-py/blob/v5.8.0/setup.py#L217-L224
+appdirs==1.4.4
+future==0.18.2
+numpy==1.19.1
+Pillow==7.2.0
+PyYAML==5.3.1
+requests==2.24.0
+# To speed this up install a distribution-specific wheel before installing
+# this package (wheels cannot be included in requirements)
+zeroc-ice==3.6.5
+
+# minimum requirements for 'omero admin start'
+omero-certificates==0.2.0
+# tables==3.6.1  # Debian9/Ubuntu1604 won't work with 3.6.1
diff --git a/requirements-ubuntu1604.txt b/requirements-ubuntu1604.txt
new file mode 100644
index 0000000..a6adc2a
--- /dev/null
+++ b/requirements-ubuntu1604.txt
@@ -0,0 +1 @@
+tables==3.5.2
diff --git a/setup.py b/setup.py
index ced6ce6..3e0667c 100755
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
    Use is subject to license terms supplied in LICENSE.txt
 
 """
-
+from glob import glob
 import os
 import sys
 
@@ -25,6 +25,26 @@ def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
 
+def parse_requirements(fname):
+    """
+    Utility function to parse requirements.txt files.
+    """
+    with open(os.path.join(os.path.dirname(__file__), fname)) as f:
+        txt = f.read().splitlines()
+        return [
+            line.strip() for line in txt if not line.strip().startswith('#')]
+
+
+def get_extras_require():
+    extras = {}
+    requirements_files = [os.path.basename(g) for g in glob(
+        os.path.join(os.path.dirname(__file__), 'requirements-*.txt'))]
+    for fname in requirements_files:
+        if fname != 'requirements-pinned.txt':
+            extras[fname[13:-4]] = parse_requirements(fname)
+    return extras
+
+
 setup(name="omero-server",
       version=osv,
       description="CLI plugin for managing an OMERO.server",
@@ -48,17 +68,8 @@ def read(fname):
       license='GPLv2+',
       packages=find_packages(exclude=("test",))+["omero.plugins"],
       python_requires='>=3',
-      install_requires=[
-          # requires Ice (use wheel for faster installs)
-          'omero-py',
-          # minimum requirements for `omero admin start`
-          'omero-certificates',
-      ],
+      install_requires=parse_requirements('requirements-pinned.txt'),
       include_package_data=True,
       tests_require=['pytest'],
-      extras_require={
-        "debian9": ["tables<3.6"],
-        "ubuntu1604": ["tables<3.6"],
-        "default": ["tables"],
-      }
+      extras_require=get_extras_require(),
       )

From c7fa0704b006e7e3e272f29385b107d85e5643ba Mon Sep 17 00:00:00 2001
From: Simon Li <spli@dundee.ac.uk>
Date: Tue, 22 Sep 2020 15:59:30 +0100
Subject: [PATCH 2/3] Include *.txt in Dockerfile

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index 2021341..ac07d78 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,6 +18,7 @@ USER tox
 COPY --chown=tox:tox *.py /src/
 COPY --chown=tox:tox README.rst /src
 COPY --chown=tox:tox MANIFEST.in /src
+COPY --chown=tox:tox *.txt /src/
 COPY --chown=tox:tox omero /src/omero
 COPY --chown=tox:tox omeroserver /src/omeroserver
 WORKDIR /src

From 8027e95ba9a9373543e7c35d174ecd2790f9ec50 Mon Sep 17 00:00:00 2001
From: Simon Li <spli@dundee.ac.uk>
Date: Tue, 22 Sep 2020 16:08:57 +0100
Subject: [PATCH 3/3] MANIFEST.in: requirements-*.txt

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index 42eb410..9756fe8 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1 +1,2 @@
 include LICENSE.txt
+include requirements-*.txt