From 83d682ba67ee9f04ed5b2793ca277dd6c597c145 Mon Sep 17 00:00:00 2001
From: bricoletc <bletcher@ebi.ac.uk>
Date: Mon, 24 Jan 2022 21:49:38 +0000
Subject: [PATCH] Update README and fixup setups

* Add licence file and python requires to setup.cfg
* Fix-up setup.py
* Update README to reflect new backend build strategy
---
 README.md | 39 ++++++++++++++++++++++++++-------------
 setup.cfg |  2 ++
 setup.py  |  7 +++++--
 3 files changed, 33 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index edde10f..a51fe00 100644
--- a/README.md
+++ b/README.md
@@ -44,35 +44,48 @@ singularity exec "$URI" gramtools
 
 #### Latest release
 
+We recommend installing inside a virtual environment:
 ```sh
-VERSION="1.7.0"
-wget -O - "https://github.com/iqbal-lab-org/gramtools/releases/download/v${VERSION}/gramtools-${VERSION}.tar.gz" | tar xfz -
-pip install "./gramtools-${VERSION}"
+python -m venv venv_gramtools && source venv_gramtools/bin/activate
 ```
-The latest release includes a precompiled binary for Linux. This will be used if it works on your machine, else it will get compiled during the installation.
 
-We recommend installing inside a virtual environment:
 ```sh
-python -m venv gram_ve && source gram_ve/bin/activate
-pip install pip==20.0.2
-pip install gramtools-${VERSION}
+VERSION="1.9.0"
+wget -O - "https://github.com/iqbal-lab-org/gramtools/releases/download/v${VERSION}/gramtools-${VERSION}.tar.gz" | tar xfz -
+pip install ./gramtools-"${VERSION}"
 ```
+gramtools contains a compiled backend component. The latest release includes a
+precompiled backend for Linux.  Run `gramtools` to see if it is compatible with your
+machine. If gramtools tells you it is not, run the following to compile the backend on
+your machine:
+
+```
+pip install conan
+bash ./gramtools-"${VERSION}"
+```
+
+Please report any errors via the [issue tracker](https://github.com/iqbal-lab-org/gramtools/issues).
 
 #### Latest source
 
+This will always compile the binary.
+
 ```sh
-pip install git+https://github.com/iqbal-lab-org/gramtools
+git clone https://github.com/iqbal-lab-org/gramtools
+pip install conan
+bash ./gramtools/build.sh
+pip install ./gramtools
 ```
-This will always compile the binary.
 
 #### Requirements
 
-`Python >= 3.6` and `pip >= 20.0.2`
+`Python >= 3.6` and `pip >= 20.0.2`.
 
-If the binary needs to be compiled, you also need `CMake >= 3.1.2` and a C++17 
+If the backend needs to be compiled, you also need `CMake >= 3.1.2` and a C++17 
 compatible compiler: `g++ >=8` (tested) or `clang >=7` (untested).
 
-For `gramtools discover` to work, you additionally need `R` and `Perl` available at runtime.
+For `gramtools discover` to work, you additionally need to install `py-cortex-api` (it
+is installable via PyPi/pip) and have `R` and `Perl` on your $PATH.
 
 ## Usage
 
diff --git a/setup.cfg b/setup.cfg
index 907dc4e..8ad8de4 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -8,6 +8,7 @@ long_description = file: README.md
 long_description_content_type = text/markdown
 url = https://github.com/iqbal-lab-org/gramtools
 licence = MIT
+licence_file = LICENCE
 
 [options]
 packages = find:
@@ -17,6 +18,7 @@ install_requires =
     Cython == 0.29.16
     pysam == 0.15.4
     cluster_vcf_records >= 0.9.2
+python_requires = >=3.6
 
 [options.entry_points]
 console_scripts =
diff --git a/setup.py b/setup.py
index d620937..61cab1b 100644
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,9 @@
+import unittest
+import setuptools
+
 # For pysam to use existing htslib compiled by the backend
-os.environ["HTSLIB_LIBRARY_DIR"] = str(cmake_dir / "libgramtools" / "lib")
-os.environ["HTSLIB_INCLUDE_DIR"] = str(cmake_dir / "libgramtools" / "include")
+# os.environ["HTSLIB_LIBRARY_DIR"] = str(cmake_dir / "libgramtools" / "lib")
+# os.environ["HTSLIB_INCLUDE_DIR"] = str(cmake_dir / "libgramtools" / "include")
 
 
 def _test_backend(root_dir):