Add linting

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+max-line-length = 115

.github/workflows/linting.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - uses: pre-commit/[email protected]

.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile=black

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-ast
+    -   id: check-case-conflict
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    -   id: check-yaml
+    -   id: debug-statements
+
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+    -   id: flake8
+        args: ["--ignore=E203,W503"]
+
+-   repo: https://github.com/timothycrosley/isort
+    rev: 5.9.3
+    hooks:
+    -   id: isort
+
+-   repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+    -   id: black

LICENSE

@@ -27,4 +27,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

README.md

@@ -1,4 +1,3 @@
 # Workflows
 
 Repository of workflows for the FXI beamline.
-

end_of_run_workflow.py

@@ -1,5 +1,5 @@
 import prefect
-from prefect import task, Flow, Parameter
+from prefect import Flow, Parameter, task
 from prefect.tasks.prefect import create_flow_run
 
 
@@ -15,12 +15,9 @@ def log_completion():
     validation_flow = create_flow_run(
         flow_name="general-data-validation",
         project_name="FXI",
-        parameters={"beamline_acronym": "fxi" ,"uid": uid}
+        parameters={"beamline_acronym": "fxi", "uid": uid},
     )
     export_flow = create_flow_run(
-        flow_name="export",
-        project_name="FXI",
-        parameters={"uid": uid}
+        flow_name="export", project_name="FXI", parameters={"uid": uid}
     )
     log_completion(upstream_tasks=[validation_flow, export_flow])
-

export.py

@@ -1,14 +1,14 @@
-import databroker
 import datetime
+import os
+from pathlib import Path
+
+import databroker
 import h5py
 import numpy as np
-import os
 import pandas as pd
 import prefect
-
-from pathlib import Path
 from PIL import Image
-from prefect import task, Flow, Parameter
+from prefect import Flow, Parameter, task
 
 
 @task
@@ -69,9 +69,9 @@ def get_img(run, det="Andor", sli=[]):
     "Take in a Header and return a numpy array of detA1 image(s)."
     det_name = f"{det}_image"
     if len(sli) == 2:
-        img = np.array(list(run['primary']['data'][det_name])[sli[0] : sli[1]])
+        img = np.array(list(run["primary"]["data"][det_name])[sli[0] : sli[1]])
     else:
-        img = np.array(list(run['primary']['data'][det_name]))
+        img = np.array(list(run["primary"]["data"][det_name]))
     return np.squeeze(img)
 
 
@@ -92,17 +92,17 @@ def bin_ndarray(ndarray, new_shape=None, operation="mean"):
      [262 270 278 286 294]
      [342 350 358 366 374]]
     """
-    if new_shape == None:
+    if new_shape is None:
         s = np.array(ndarray.shape)
         s1 = np.int32(s / 2)
         new_shape = tuple(s1)
     operation = operation.lower()
-    if not operation in ["sum", "mean"]:
+    if operation not in ["sum", "mean"]:
         raise ValueError("Operation not supported.")
     if ndarray.ndim != len(new_shape):
         raise ValueError("Shape mismatch: {} -> {}".format(ndarray.shape, new_shape))
     compression_pairs = [(d, c // d) for d, c in zip(new_shape, ndarray.shape)]
-    flattened = [l for p in compression_pairs for l in p]
+    flattened = [ell for p in compression_pairs for ell in p]
     ndarray = ndarray.reshape(flattened)
     for i in range(len(new_shape)):
         op = getattr(ndarray, operation)
@@ -727,7 +727,8 @@ def export_raster_2D_2(run, binning=4, filepath="", **kwargs):
                 y_list[j] * pix * img_sizeY / 1000,
             ]
             pos_file.append(
-                f"{x_list[i]:3.0f}\t{y_list[j]:3.0f}\t{x_list[i]*pix*img_sizeX/1000:3.3f}\t\t{y_list[j]*pix*img_sizeY/1000:3.3f}\n"
+                f"{x_list[i]:3.0f}\t{y_list[j]:3.0f}\t{x_list[i]*pix*img_sizeX/1000:3.3f}\t\t"
+                + f"{y_list[j]*pix*img_sizeY/1000:3.3f}\n"
             )
             index = index + 1
     s = img_patch.shape
@@ -804,7 +805,8 @@ def export_raster_2D(run, binning=4, filepath="", **kwargs):
                 y_list[j] * pix * img_sizeY / 1000,
             ]
             pos_file.append(
-                f"{x_list[i]:3.0f}\t{y_list[j]:3.0f}\t{x_list[i]*pix*img_sizeX/1000:3.3f}\t\t{y_list[j]*pix*img_sizeY/1000:3.3f}\n"
+                f"{x_list[i]:3.0f}\t{y_list[j]:3.0f}\t{x_list[i]*pix*img_sizeX/1000:3.3f}\t\t"
+                + f"{y_list[j]*pix*img_sizeY/1000:3.3f}\n"
             )
             index = index + 1
     s = img_patch.shape

print_scanid.py

@@ -1,18 +1,20 @@
 import databroker
 import prefect
-from prefect import task, Flow
+from prefect import Flow, task
+
 
 @task
 def print_scanid():
     client = databroker.from_profile("nsls2", username=None)
-    scan_id = client['fxi'][-1].start['scan_id']
+    scan_id = client["fxi"][-1].start["scan_id"]
     logger = prefect.context.get("logger")
     logger.info(f"Scan ID: {scan_id}")
 
+
 with Flow("scan_id") as flow:
     print_scanid()
 
-#flow.register(project_name='TST',
+# flow.register(project_name='TST',
 #              labels=['fxi-2022-2.2'],
 #              add_default_labels=False,
 #              set_schedule_active=False)

pyproject.toml

@@ -0,0 +1,9 @@
+[tool.black]
+line-length = 88
+exclude = '''
+(
+  /(
+    | \.git
+  )/
+)
+'''