Run pre-commit

.pre-commit-config.yaml

@@ -0,0 +1,59 @@
+default_stages: [commit, push]
+exclude: (^.github/|^docs/|^images/|^notebooks/py_scripts/|^tests/)
+# Current tests/__init__ violates many flake8. Excluding pending change to conftest
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files # prevent giant files from being committed
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+        description: Forces to replace line ending by the UNIX 'lf' character.
+
+  # black
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+        args:
+          - --line-length=88
+
+  # isort
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        description: Sorts imports in an alphabetical order
+
+  # flake8
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: # arguments to configure flake8
+          # making isort line length compatible with black
+          - "--max-line-length=88"
+          - "--max-complexity=18"
+          - "--select=B,C,E,F,W,T4,B9"
+
+          # these are errors that will be ignored by flake8
+          # https://www.flake8rules.com/rules/{code}.html
+          - "--ignore=E203,E501,W503,W605,E402"
+          # E203 - Colons should not have any space before them.
+          #        Needed for list indexing
+          # E501 - Line lengths are recommended to be no greater than 79 characters.
+          #        Needed as we conform to 88
+          # W503 - Line breaks should occur after the binary operator.
+          #        Needed because not compatible with black
+          # W605 - a backslash-character pair that is not a valid escape sequence now
+          #        generates a DeprecationWarning. This will eventually become a SyntaxError.
+          #        Needed because we use \d as an escape sequence
+          # E402 - Place module level import at the top.
+          #        Needed to prevent circular import error

README.md

@@ -1,7 +1,7 @@
 # DataJoint Workflow - Calcium Imaging
 
 Workflow for calcium imaging data acquired with
-[ScanImage](http://scanimage.vidriotechnologies.com),  
+[ScanImage](http://scanimage.vidriotechnologies.com),
 [Scanbox](https://scanbox.org), or `Nikon NIS` software and processed with
 [Suite2p](https://github.com/MouseLand/suite2p) or
 [CaImAn](https://github.com/flatironinstitute/CaImAn).

docker/Dockerfile.dev

@@ -6,10 +6,10 @@ COPY ./workflow-calcium-imaging/docker/apt_requirements.txt /tmp/
 RUN /entrypoint.sh echo "Installed dependencies."
 
 # Install Caiman
-RUN git clone --branch master https://github.com/datajoint-company/CaImAn 
+RUN git clone --branch master https://github.com/datajoint-company/CaImAn
 WORKDIR /main/CaImAn
 RUN conda install -n base -c conda-forge -y mamba
-RUN /bin/bash -c 'mamba env update --n base --file environment.yml' 
+RUN /bin/bash -c 'mamba env update --n base --file environment.yml'
 # Suite2p requires np.__version__ == 1.21
 RUN pip install numpy==1.21
 RUN pip install .
@@ -42,4 +42,4 @@ RUN pip install -r /main/workflow-calcium-imaging/requirements_test.txt
 
 WORKDIR /main/workflow-calcium-imaging
 
-ENTRYPOINT ["tail", "-f", "/dev/null"]
+ENTRYPOINT ["tail", "-f", "/dev/null"]

docker/Dockerfile.test

@@ -6,10 +6,10 @@ COPY ./workflow-calcium-imaging/docker/apt_requirements.txt /tmp/
 RUN /entrypoint.sh echo "Installed dependencies."
 
 # Install Caiman
-RUN git clone --branch master https://github.com/datajoint-company/CaImAn 
+RUN git clone --branch master https://github.com/datajoint-company/CaImAn
 WORKDIR /main/CaImAn
 RUN conda install -n base -c conda-forge -y mamba
-RUN /bin/bash -c 'mamba env update --n base --file environment.yml' 
+RUN /bin/bash -c 'mamba env update --n base --file environment.yml'
 # Suite2p requires np.__version__ == 1.21
 RUN pip install numpy==1.21
 RUN pip install .
@@ -54,4 +54,4 @@ RUN rm -f /main/workflow-calcium-imaging/dj_local_conf.json
 RUN pip install /main/workflow-calcium-imaging
 RUN pip install -r /main/workflow-calcium-imaging/requirements_test.txt
 
-WORKDIR /main/workflow-calcium-imaging
+WORKDIR /main/workflow-calcium-imaging

docker/apt_requirements.txt

@@ -1,8 +1,8 @@
-git
-gcc
-g++
 ffmpeg
+g++
+gcc
+git
+libhdf5-dev
 libsm6
 libxext6
-libhdf5-dev
 pkg-config

notebooks/00-data-download-optional.ipynb

@@ -42,6 +42,7 @@
    "source": [
     "import os\n",
     "import djarchive_client\n",
+    "\n",
     "client = djarchive_client.client()"
    ]
   },
@@ -90,7 +91,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mkdir /tmp/example_data"
+    "mkdir / tmp / example_data"
    ]
   },
   {
@@ -107,7 +108,8 @@
    "outputs": [],
    "source": [
     "from workflow_calcium_imaging import version\n",
-    "revision = version.__version__.replace('.', '_')\n",
+    "\n",
+    "revision = version.__version__.replace(\".\", \"_\")\n",
     "revision"
    ]
   },
@@ -124,7 +126,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "client.download('workflow-calcium-imaging-test-set', target_directory='/tmp/example_data', revision=revision)"
+    "client.download(\n",
+    "    \"workflow-calcium-imaging-test-set\",\n",
+    "    target_directory=\"/tmp/example_data\",\n",
+    "    revision=revision,\n",
+    ")"
    ]
   },
   {

notebooks/01-configure.ipynb

@@ -20,7 +20,9 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "if os.path.basename(os.getcwd()) == \"notebooks\": os.chdir(\"..\")\n",
+    "\n",
+    "if os.path.basename(os.getcwd()) == \"notebooks\":\n",
+    "    os.chdir(\"..\")\n",
     "import datajoint as dj"
    ]
   },
@@ -49,7 +51,8 @@
    "outputs": [],
    "source": [
     "import getpass\n",
-    "dj.config[\"database.host\"] = \"{YOUR_HOST}\" # CodeBook users should omit this\n",
+    "\n",
+    "dj.config[\"database.host\"] = \"{YOUR_HOST}\"  # CodeBook users should omit this\n",
     "dj.config[\"database.user\"] = \"{YOUR_USERNAME}\"\n",
     "dj.config[\"database.password\"] = getpass.getpass()  # enter the password securely"
    ]
@@ -145,8 +148,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dj.config['custom']['imaging_root_data_dir'] = '/tmp/example_data' # local download\n",
-    "dj.config['custom']['imaging_root_data_dir'] = '/home/inbox/0_1_0a2/' # on CodeBook"
+    "dj.config[\"custom\"][\"imaging_root_data_dir\"] = \"/tmp/example_data\"  # local download\n",
+    "dj.config[\"custom\"][\"imaging_root_data_dir\"] = \"/home/inbox/0_1_0a2/\"  # on CodeBook"
    ]
   },
   {

notebooks/02-workflow-structure-optional.ipynb

@@ -24,7 +24,9 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "if os.path.basename(os.getcwd()) == \"notebooks\": os.chdir(\"..\")"
+    "\n",
+    "if os.path.basename(os.getcwd()) == \"notebooks\":\n",
+    "    os.chdir(\"..\")"
    ]
   },
   {