From f91dceafcc1732f8196af4e580f33f4c6aec86e9 Mon Sep 17 00:00:00 2001
From: jthetzel <jthetzel@gmail.com>
Date: Sat, 28 Nov 2020 11:01:45 -0330
Subject: [PATCH 1/5] fix: Configure conda to use local .conda directory

`conda create` creates the $HOME/.conda directory but does
not prepend it conda config. Closes #377
---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 2b939ee0..c4aeca92 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -15,6 +15,8 @@ USER pims
 # Set up the initial conda environment
 COPY --chown=pims:pims environment.yml /src/environment.yml
 WORKDIR /src
+RUN conda config --prepend envs_dirs $HOME/.conda/envs
+RUN conda config --prepend pkgs_dirs $HOME/.conda/pkgs
 RUN conda env create -f environment.yml \
     && conda clean -tipsy
 

From fa3835803009d3e165977f4236a2d6cc56f58937 Mon Sep 17 00:00:00 2001
From: jthetzel <jthetzel@gmail.com>
Date: Sat, 28 Nov 2020 11:31:29 -0330
Subject: [PATCH 2/5] fix: Rename loci.formats in to in_

Attribute name automatically mangled due to conflict.
https://github.com/soft-matter/pims/issues/373#issuecomment-735013243
---
 pims/bioformats.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pims/bioformats.py b/pims/bioformats.py
index 95d21dc1..4e1807dd 100644
--- a/pims/bioformats.py
+++ b/pims/bioformats.py
@@ -361,7 +361,7 @@ def __init__(self, filename, meta=True, java_memory='512m',
         # patch for issue with ND2 files and the Chunkmap implemented in 5.4.0
         # See https://github.com/openmicroscopy/bioformats/issues/2955
         # circumventing the reserved keyword 'in'
-        mo = getattr(loci.formats, 'in').DynamicMetadataOptions()
+        mo = getattr(loci.formats, 'in_').DynamicMetadataOptions()
         mo.set('nativend2.chunkmap', 'False')  # Format Bool as String
         self.rdr.setMetadataOptions(mo)
 

From e77ea9c79aa8085ec51421c1617c9842e49e3bd8 Mon Sep 17 00:00:00 2001
From: jthetzel <jthetzel@gmail.com>
Date: Sat, 28 Nov 2020 12:55:26 -0330
Subject: [PATCH 3/5] fix: Call `imageio_get_ffmpeg_exe` to determine if ffmpeg
 available

Importing `imageio_ffmpeg` succeeds even if ffmpeg executable is not
available. This additional check is required when checking if
ffmpeg related tests should be skipped. Closes #379.
---
 pims/imageio_reader.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pims/imageio_reader.py b/pims/imageio_reader.py
index 4d58f0fa..f4322210 100644
--- a/pims/imageio_reader.py
+++ b/pims/imageio_reader.py
@@ -15,6 +15,10 @@
     import imageio_ffmpeg
 except ImportError:
     imageio_ffmpeg = None
+try:
+    imageio_ffmpeg.get_ffmpeg_exe()
+except RuntimeError:
+    imageio_ffmpeg = None
 
 
 def available():

From 65b20f48d65cb222e6928e8042c0a77b0d0f435b Mon Sep 17 00:00:00 2001
From: jthetzel <jthetzel@gmail.com>
Date: Sat, 28 Nov 2020 13:52:50 -0330
Subject: [PATCH 4/5] fix: Try/except AttributeName logic for `loci.formats.in`
 mangling

---
 pims/bioformats.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pims/bioformats.py b/pims/bioformats.py
index 4e1807dd..05553b1c 100644
--- a/pims/bioformats.py
+++ b/pims/bioformats.py
@@ -361,7 +361,11 @@ def __init__(self, filename, meta=True, java_memory='512m',
         # patch for issue with ND2 files and the Chunkmap implemented in 5.4.0
         # See https://github.com/openmicroscopy/bioformats/issues/2955
         # circumventing the reserved keyword 'in'
-        mo = getattr(loci.formats, 'in_').DynamicMetadataOptions()
+        try:
+            mo = getattr(loci.formats, 'in').DynamicMetadataOptions()
+        except AttributeError:
+            # Attribute name conflict causes mangling of `in` to `in_`
+            mo = getattr(loci.formats, 'in_').DynamicMetadataOptions()
         mo.set('nativend2.chunkmap', 'False')  # Format Bool as String
         self.rdr.setMetadataOptions(mo)
 

From 37bf9183b28934e28a8720c7689d1ceb3163d7ce Mon Sep 17 00:00:00 2001
From: jthetzel <jthetzel@gmail.com>
Date: Sat, 28 Nov 2020 13:56:56 -0330
Subject: [PATCH 5/5] fix: Move get_ffmpeg_exe call within imageio_ffmpeg
 import block

---
 pims/imageio_reader.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pims/imageio_reader.py b/pims/imageio_reader.py
index f4322210..15bdfd88 100644
--- a/pims/imageio_reader.py
+++ b/pims/imageio_reader.py
@@ -13,12 +13,12 @@
     imageio = None
 try:
     import imageio_ffmpeg
+    try:
+        imageio_ffmpeg.get_ffmpeg_exe()
+    except RuntimeError:
+        imageio_ffmpeg = None
 except ImportError:
     imageio_ffmpeg = None
-try:
-    imageio_ffmpeg.get_ffmpeg_exe()
-except RuntimeError:
-    imageio_ffmpeg = None
 
 
 def available():