Merge pull request #213 from broadinstitute/dev

update docs w/ troubleshooting. update release.yml

docs/index.rst

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 The Activity-by-Contact (ABC) Model for predicting enhancer-gene regulatory interactions
-========================================================
+========================================================================================
 
 The Activity-by-Contact (ABC) model predicts which enhancers regulate which genes in a given cell type, based on a combination of input datasets representing enhancer activity and 3D enhancer-promoter contact frequency [1].
 
@@ -47,6 +47,7 @@ v0.2 (version for [1])
    usage/getting_started
    usage/methods
    usage/scATAC
+   usage/troubleshooting
 
 
 .. toctree::

docs/usage/troubleshooting.rst

@@ -0,0 +1,12 @@
+Troubleshooting
+===============
+
+Conda Env Building Issues
+-----------------------------
+Building the conda environment can take a lot of resources, especially if you're not using `mamba`. Make sure the process isn't being killed 
+(e.g because it's taking up too many resources in a shared environment). If it is, make sure you try building the environment with more resources. 
+
+If you're on MacOSX, make sure to remove some of the requirements in abcenv.yml. Those requirements to delete are flagged in the file.
+
+If there are incompatibility issues, try building off the 'release.yml' conda environment.
+

workflow/envs/release.yml

@@ -80,6 +80,7 @@ dependencies:
   - dropbox=11.36.2=pyhd8ed1ab_0
   - eido=0.2.2=pyhd8ed1ab_0
   - exceptiongroup=1.2.0=pyhd8ed1ab_2
+  - execnet=2.0.2=pyhd8ed1ab_0
   - expat=2.5.0=hcb278e6_1
   - filechunkio=1.8=py_2
   - fmt=10.2.1=h00ab1b0_0
@@ -293,6 +294,7 @@ dependencies:
   - pysftp=0.2.9=py_1
   - pysocks=1.7.1=pyha2e5f31_6
   - pytest=8.0.2=pyhd8ed1ab_0
+  - pytest-xdist=3.5.0=pyhd8ed1ab_0
   - python=3.10.13=hd12c33a_1_cpython
   - python-dateutil=2.9.0=pyhd8ed1ab_0
   - python-fastjsonschema=2.19.1=pyhd8ed1ab_0