fixing import error with h5py and paramiko #987

Author: carsen-stringer

README.md

@@ -59,7 +59,9 @@ Pachitariu, M., Stringer, C., Schröder, S., Dipoppa, M., Rossi, L. F., Carandin
 7. Now run `python -m suite2p` and you're all set.
 8. Running the command `suite2p --version` in the terminal will print the install version of suite2p.
 
-For additional dependencies, like NWB and Scanbox support, use the command `python -m pip install suite2p[io]`.
+For additional dependencies, like h5py, NWB, Scanbox, and server job support, use the command `python -m pip install suite2p[io]`.
+
+If you are running suite2p on Windows or Linux we recommend installing ScanImage Tiff Reader with `pip install scanimage-tiff-reader`.
 
 If you have an older `suite2p` environment you can remove it with `conda env remove -n suite2p` before creating a new one.
 

suite2p/io/h5.py

@@ -3,7 +3,11 @@
 """
 import math
 
-import h5py
+try:
+    import h5py
+    HAS_H5PY=True
+except:
+    HAS_H5PY=False
 import numpy as np
 import os
 
@@ -25,6 +29,9 @@ def h5py_to_binary(ops):
             "Ly", "Lx", ops["reg_file"] or ops["raw_file"] is created binary
 
     """
+    if not HAS_H5PY:
+        raise ImportError("h5py is required for this file type, please 'pip install h5py'")
+
     ops1 = init_ops(ops)
 
     nplanes = ops1[0]["nplanes"]

suite2p/io/server.py

@@ -4,14 +4,17 @@
 import sys, os, time, glob
 from pathlib import Path
 from natsort import natsorted
-import paramiko
 import numpy as np
+try:
+    import paramiko
+    HAS_PARAMIKO = True 
+except:
+    HAS_PARAMIKO = False
 
 
 def unix_path(path):
     return str(path).replace(os.sep, "/")
 
-
 def ssh_connect(host, username, password, verbose=True):
     """ from paramiko example """
     i = 0
@@ -38,7 +41,6 @@ def ssh_connect(host, username, password, verbose=True):
             sys.exit(1)
     return ssh
 
-
 def send_jobs(save_folder, host=None, username=None, password=None, server_root=None,
               local_root=None, n_cores=8):
     """ send each plane to compute on server separately
@@ -47,6 +49,8 @@ def send_jobs(save_folder, host=None, username=None, password=None, server_root=
     for where to save the data
 
     """
+    if not HAS_PARAMIKO:
+        raise ImportError("paramiko required, please 'pip install paramiko'")
 
     if host is None:
         raise Exception("No server specified, please edit suite2p/io/server.py")