From 084194b4612623976cb5a46cd1b47f4afbe6fdec Mon Sep 17 00:00:00 2001
From: Stephen Fleming <sjfleming@users.noreply.github.com>
Date: Tue, 31 Oct 2023 11:55:37 -0400
Subject: [PATCH] Fix bugs with report generation across platforms (#302)

---
 cellbender/remove_background/posterior.py | 11 ++++++++--
 cellbender/remove_background/report.py    | 25 ++++++++++++++---------
 cellbender/remove_background/run.py       |  1 +
 3 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/cellbender/remove_background/posterior.py b/cellbender/remove_background/posterior.py
index c421713..d99e533 100644
--- a/cellbender/remove_background/posterior.py
+++ b/cellbender/remove_background/posterior.py
@@ -1518,7 +1518,9 @@ def __repr__(self):
                 f'\n\ttotal_n_genes: {self.total_n_genes}'
                 f'\n\tmatrix_shape: {self.matrix_shape}')
 
-    def get_m_indices(self, cell_inds: np.ndarray, gene_inds: np.ndarray) -> np.ndarray:
+    def get_m_indices(self,
+                      cell_inds: Union[np.ndarray, torch.Tensor],
+                      gene_inds: Union[np.ndarray, torch.Tensor]) -> Union[np.ndarray, torch.Tensor]:
         """Given arrays of cell indices and gene indices, suitable for a sparse matrix,
         convert them to 'm' index values.
         """
@@ -1528,7 +1530,12 @@ def get_m_indices(self, cell_inds: np.ndarray, gene_inds: np.ndarray) -> np.ndar
         if not ((gene_inds >= 0) & (gene_inds < self.total_n_genes)).all():
             raise ValueError(f'Requested gene_inds out of range: '
                              f'{gene_inds[(gene_inds < 0) | (gene_inds >= self.total_n_genes)]}')
-        return cell_inds.astype(np.uint64) * self.total_n_genes + gene_inds.astype(np.uint64)
+        if type(cell_inds) == np.ndarray:
+            return cell_inds.astype(np.uint64) * self.total_n_genes + gene_inds.astype(np.uint64)
+        elif type(cell_inds) == torch.Tensor:
+            return cell_inds.type(torch.int64) * self.total_n_genes + gene_inds.type(torch.int64)
+        else:
+            raise ValueError('IndexConverter.get_m_indices received cell_inds of unkown object type')
 
     def get_ng_indices(self, m_inds: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
         """Given a list of 'm' index values, return two arrays: cell index values
diff --git a/cellbender/remove_background/report.py b/cellbender/remove_background/report.py
index f1a34cb..dfb5f90 100644
--- a/cellbender/remove_background/report.py
+++ b/cellbender/remove_background/report.py
@@ -16,6 +16,7 @@
 import subprocess
 import datetime
 import os
+import shutil
 import logging
 from typing import Dict, Optional
 
@@ -42,26 +43,30 @@
 
 
 def _run_notebook(file):
-    subprocess.run(f'cp {file} tmp.report.ipynb', shell=True)
+    shutil.copy(file, 'tmp.report.ipynb')
     subprocess.run(run_notebook_str(file='tmp.report.ipynb'), shell=True)
-    subprocess.run(f'rm tmp.report.ipynb', shell=True)
+    os.remove('tmp.report.ipynb')
     return 'tmp.report.nbconvert.ipynb'
 
 
 def _to_html(file, output) -> str:
     subprocess.run(to_html_str(file=file, output=output), shell=True)
-    subprocess.run(f'mv {file.replace(".ipynb", ".html")} {output}', shell=True)
-    subprocess.run(f'rm {file}', shell=True)
+    os.replace(file.replace(".ipynb", ".html"), output)
+    os.remove(file)
     return output
 
 
 def _postprocess_html(file: str, title: str):
-    with open(file, mode='r') as f:
-        html = f.read()
-    html = html.replace('<title>tmp.report.nbconvert</title>',
-                        f'<title>{title}</title>')
-    with open(file, mode='w') as f:
-        f.write(html)
+    try:
+        with open(file, mode='r', encoding="utf8", errors="surrogateescape") as f:
+            html = f.read()
+        html = html.replace('<title>tmp.report.nbconvert</title>',
+                            f'<title>{title}</title>')
+        with open(file, mode='w', encoding="utf8", errors="surrogateescape") as f:
+            f.write(html)
+    except:
+        logger.warning('Failed to overwrite default HTML report title. '
+                       'This is purely aesthetic and does not affect output.')
 
 
 def run_notebook_make_html(file, output) -> str:
diff --git a/cellbender/remove_background/run.py b/cellbender/remove_background/run.py
index 42cf5b4..ca2a592 100644
--- a/cellbender/remove_background/run.py
+++ b/cellbender/remove_background/run.py
@@ -43,6 +43,7 @@
 from typing import Tuple, Optional, Dict, Union
 
 import matplotlib
+import matplotlib.backends.backend_pdf  # issue #287
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt  # This needs to be after matplotlib.use('Agg')