[pip] fix numpy issue during requirements installation

README.md

@@ -65,9 +65,12 @@ git clone --recursive https://github.com/clara-genomics/AtacWorks.git
 * Install pip dependencies
 
     ```
-    pip install -r requirements-pip.txt
+    pip install -r requirements-base.txt && pip install -r requirements-macs2.txt
     ```
 
+Note: The above non-standard installation is necessary to ensure the requirements for macs2 are installed
+before macs2 itself.
+
 ### Unit tests
 
     ```
@@ -107,10 +110,7 @@ These are based on bulk ATAC-Seq data from 7 blood cell types. They are trained
 
 ### FAQ
 1. What's the preferred way for setting up the environment ?
-A. A virtual environment or conda installation is preferred. You can follow conda installation instructions on their website and then follow the instructions in the README.
-
-2. If you face "no module named numpy" error while installing requirement-pip.txt.
-A. In your terminal, run pip install numpy==<version-from-requirements-pip.txt> and then run pip install -r requirements-pip.txt. If you are running inside a conda or venv, run these commands inside your environment.
+    > A virtual environment or conda installation is preferred. You can follow conda installation instructions on their website and then follow the instructions in the README.
 
 ### Citation
 

ci/common/test-pyclaragenomics.sh

@@ -18,8 +18,7 @@ PYCLARAGENOMICS_DIR=$1
 cd $PYCLARAGENOMICS_DIR
 
 #Install external dependencies.
-python -m pip install numpy==1.17.0
-python -m pip install -r requirements-pip.txt
+pip install -r requirements-base.txt && pip install -r requirements-macs2.txt
 
 LOCAL_BIN_DIR="local_bin"
 mkdir -p $LOCAL_BIN_DIR

requirements-pip.txt → requirements-base.txt

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
 #
 # NVIDIA CORPORATION and its licensors retain all intellectual property
 # and proprietary rights in and to this software, related documentation
@@ -18,6 +18,5 @@ termcolor==1.1.0
 torch==1.2.0
 torchvision==0.3.0
 scikit-learn==0.21.3
-macs2==2.2.4
 scipy==1.3.2
 configargparse==0.15.2

requirements-macs2.txt

@@ -0,0 +1,11 @@
+#
+# Copyright (c) 2020, NVIDIA CORPORATION.  All rights reserved.
+#
+# NVIDIA CORPORATION and its licensors retain all intellectual property
+# and proprietary rights in and to this software, related documentation
+# and any modifications thereto.  Any use, reproduction, disclosure or
+# distribution of this software and related documentation without an express
+# license agreement from NVIDIA CORPORATION is strictly prohibited.
+#
+
+macs2==2.2.4