Bug Fixes

.gitignore

@@ -1 +1,15 @@
+
+/.idea
 *.pyc
+
+/build
+/synister.egg-info
+/src
+
+/data/fafb_v3/mongodb.ini
+
+/singularity/requirements.txt
+/singularity/setup.py
+/singularity/synister
+/singularity/synister.img
+/singularity/src

README.md

@@ -30,13 +30,16 @@ useful to train and predict in other datasets.
 
 ### Installation
 
-1. Singularity
+You need to build a Singularity container and a conda environment.
+
+#### Singularity
+Install [Singularity](https://github.com/sylabs/singularity/blob/main/INSTALL.md) and then run this:
 ```console
 cd singularity
 make
 ```
-
-2. Conda
+#### Conda
+Create a conda environment with:
 ```
 conda create -n synister -c conda-forge -c funkey python numpy scipy cython pylp pytorch-gpu
 conda activate synister

requirements.txt

@@ -11,9 +11,9 @@ tqdm
 tensorboardX
 notebook==6.1.4
 zarr
-git+git://github.com/nilsec/pymaid@master
+git+https://github.com/nilsec/pymaid@master
 -e git+https://github.com/funkey/gunpowder@754607abcd3c84ec28c0d2ea257b969934ce986d#egg=gunpowder
--e git+https://github.com/funkelab/daisy@0.3-dev#egg=daisy
+-e git+https://github.com/funkelab/daisy@master#egg=daisy
 -e git+https://github.com/funkelab/funlib.learn.torch@636813e60d48379d078b5458e40bdf23269631b3#egg=funlib.learn.torch
 -e git+https://github.com/funkelab/funlib.show.neuroglancer@master#egg=funlib.show.neuroglancer
 -e git+https://github.com/funkelab/funlib.math@master#egg=funlib.math

singularity/Singularity

@@ -40,11 +40,10 @@ rm -rf /var/lib/apt/lists/*
 
 # install conda
 
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.10.3-Linux-x86_64.sh -O miniconda.sh
 bash miniconda.sh -b -p /miniconda
 PATH="/miniconda/bin:$PATH"
 conda config --set always_yes yes --set changeps1 no
-conda update -q conda
 conda info -a
 conda install python=3.6
 
@@ -124,7 +123,7 @@ python setup.py build_ext --inplace
 PYTHONPATH=${FUNLIB_LEARN_ROOT}:$PYTHONPATH
 
 # install pytorch
-conda install pytorch torchvision cudatoolkit=10.2 -c pytorch
+conda install pytorch=1.10.2 torchvision==0.11.3 cudatoolkit=11.3 -c pytorch
 
 # install synister
 cd /src/synister
@@ -134,7 +133,7 @@ PYTHONPATH=/src/synister:$PYTHONPATH
 
 pip install mahotas
 pip install pymongo
-pip install opencv-python
+pip install opencv-python==4.2.0.34
 pip install iteration_utilities
 
 %environment

synister/synister_db.py

@@ -30,11 +30,40 @@ def __init__(self, credentials, db_name):
             self.credentials["host"] = config.get("Credentials", "host")
             self.credentials["port"] = config.get("Credentials", "port")
 
-        self.auth_string = 'mongodb://{}:{}@{}:{}'.format(self.credentials["user"],
-                                                          self.credentials["password"],
-                                                          self.credentials["host"],
-                                                          self.credentials["port"])
+            self.connection = {}
+            self.connection["is_srv"] = config.get("Connection", "is_srv").lower()
+            if self.connection["is_srv"] == "true":
+                self.connection["is_srv"] = True
+            elif self.connection["is_srv"] == "false":
+                self.connection["is_srv"] = False
+            else:
+                raise ValueError('"is_srv" must be "true" or "false".')
+
+            self.connection["options"] = config.get("Connection", "options")
+
+        auth_string_0 = 'mongodb'
+
+        auth_string_template_1 = '://{user:s}:{password:s}@{host:s}'
+
+        auth_string_1 = auth_string_template_1.format(
+            user=self.credentials["user"],
+            password=self.credentials["password"],
+            host=self.credentials["host"])
+
+        if self.connection["is_srv"]:
+            auth_string_0 += '+srv'
+        elif len(self.credentials["port"]) > 0:
+            try:
+                int(self.credentials["port"])
+                auth_string_1 += ':' + self.credentials["port"]
+            except ValueError:
+                raise ValueError('"port" must only contains numeric characters.')
+
+        self.auth_string = auth_string_0 + auth_string_1
+
+        if (len(self.connection["options"]) > 0) and self.connection["options"].__contains__('='):
 
+            self.auth_string += '/?' + self.connection["options"]
 
         self.collections = ["synapses", "skeletons", "hemi_lineages", "meta"]