update build image for hatch

Author: mattcieslak

.circleci/config.yml

@@ -4,7 +4,7 @@ version: 2.1
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennlinc/babs_tests:datalad0.17.2_v5
+    - image: pennlinc/babs_testing:0.1
 
 # TODO:
 # runinstall: &runinstall
@@ -13,7 +13,7 @@ version: 2.1
 # TODO: add tests from flake8
 
 jobs:
-  pytest:    # run pytest
+  pytest: # run pytest
     <<: *dockersetup
     resource_class: xlarge
     working_directory: /home/circleci/src/babs
@@ -26,13 +26,13 @@ jobs:
           command: |
             pip install .[tests]
             pytest -n 6 -sv
-  
-  deployable:  # checkpoint of deployable: requires all success
+
+  deployable: # checkpoint of deployable: requires all success
     <<: *dockersetup
     steps:
       - run: echo Deploying!
 
-  deploy_pypi:   # deploy to pypi
+  deploy_pypi: # deploy to pypi
     <<: *dockersetup
     working_directory: /tmp/src/babs
     steps:
@@ -49,7 +49,6 @@ jobs:
             python3 -m twine upload dist/*
         # NOTE: if want to test with test pypi, add `--repository testpypi` after `twine upload`
 
-
 workflows:
   # version: 2
   build_test_deploy:
@@ -61,19 +60,19 @@ workflows:
           #  - build
           filters:
             tags:
-              only: /.*/    # i.e., all branches and tags
+              only: /.*/ # i.e., all branches and tags
       - deployable:
-          requires:    # should require all jobs' success before deploying
+          requires: # should require all jobs' success before deploying
             - pytest
-          filters:    # run when main branch + any tags
+          filters: # run when main branch + any tags
             branches:
               only: main
             tags:
               only: /.*/
       - deploy_pypi:
           requires:
             - deployable
-          filters:   # runs for no branches but runs for any tags
+          filters: # runs for no branches but runs for any tags
             branches:
               ignore: /.*/
             tags:

Dockerfile

@@ -2,9 +2,9 @@ FROM ubuntu:22.04
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    ca-certificates \
-                    bzip2 \
-                    curl \
+    ca-certificates \
+    bzip2 \
+    curl \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -33,10 +33,10 @@ ENV PATH=/opt/conda/envs/babs/bin:$PATH
 RUN git config --global user.name "CircleCI" \
     && git config --global user.email "circleci@example.com"
 
-# install BABS
-COPY . $HOME/babs
-WORKDIR $HOME/babs
-RUN pip install .[tests]
+# # install BABS
+# COPY . $HOME/babs
+# WORKDIR $HOME/babs
+# RUN pip install .[tests]
 
 # # pytest BABS
 # RUN pytest ~/babs

babs/babs.py

@@ -179,8 +179,8 @@ def datalad_save(self, path, message=None):
         # ^^ number of dicts in list `statuses` = len(path)
         # check that all statuses returned are "okay":
         # below is from cubids
-        saved_status = set([status['status'] for status in statuses])
-        if saved_status.issubset(set(['ok', 'notneeded'])) is False:
+        saved_status = {status['status'] for status in statuses}
+        if saved_status.issubset({'ok', 'notneeded'}) is False:
             # exists element in `saved_status` that is not "ok" or "notneeded"
             # ^^ "notneeded": nothing to save
             raise Exception('`datalad save` failed!')
@@ -1377,7 +1377,7 @@ def babs_status(
                                         to_print += ', ' + ses
                                     to_print += (
                                         ' was requested, as this job is running,'
-                                        + " BABS won't resubmit this job."
+                                        " BABS won't resubmit this job."
                                     )
                                     # NOTE: removed "and `--reckless` was not specified, "
                                     #   can add this ^^ back after supporting `--reckless` in CLI
@@ -1577,7 +1577,8 @@ def babs_status(
                                         username_lowercase,
                                         self.type_system,
                                     )
-                                    df_job_updated.at[i_job, 'job_account'] = msg_job_account
+                                    raise Exception('This should be impossible to reach')
+                                    # df_job_updated.at[i_job, 'job_account'] = msg_job_account
 
                 # Collect all to-be-resubmitted tasks into a single DataFrame
                 df_job_resubmit = df_job_updated[df_job_updated['needs_resubmit'] == True].copy()

babs/template_test_job.py

@@ -11,24 +11,29 @@
 def cli():
     parser = argparse.ArgumentParser()
     parser.add_argument(
-        '--path-workspace', '--path_workspace',
+        '--path-workspace',
+        '--path_workspace',
         help='The path of ephemeral compute workspace',
-        required=True)
+        required=True,
+    )
     parser.add_argument(
-        '--path-check-setup', '--path_check_setup',
+        '--path-check-setup',
+        '--path_check_setup',
         help='The path to analysis/code/check_setup folder',
-        required=True)
+        required=True,
+    )
 
     return parser
 
+
 def main():
     # Get arguments:
     args = cli().parse_args()
 
     # Prepare the yaml file:
     fn_yaml = op.join(args.path_check_setup, 'check_env.yaml')
     if op.exists(fn_yaml):
-        os.remove(fn_yaml)   # remove it
+        os.remove(fn_yaml)  # remove it
     yaml_file = open(fn_yaml, 'w')
 
     # Initialize the dict:
@@ -38,40 +43,38 @@ def main():
     flag_writable = os.access(args.path_workspace, os.W_OK)
     config['workspace_writable'] = flag_writable
     # change to the version that `read_yaml()` from babs/utils.py can read:
-    if flag_writable:   # True
+    if flag_writable:  # True
         str_writable = 'true'
     else:
         str_writable = 'false'
-    yaml_file.write(
-        'workspace_writable: ' + str_writable + '\n')
+    yaml_file.write('workspace_writable: ' + str_writable + '\n')
 
     # Which python in current env:
     # assume the python is installed; otherwise this script cannot be run:
     config['which_python'] = sys.executable
-    yaml_file.write(
-        "which_python: '" + sys.executable + "'\n")
+    yaml_file.write("which_python: '" + sys.executable + "'\n")
 
     # Check each dependent packages' versions:
     config['version'] = {}
     yaml_file.write('version:\n')
     # What packages' versions to check:
-    what_versions = {'datalad': 'datalad --version',
-                     'git': 'git --version',
-                     'git-annex': 'git-annex version',
-                     'datalad_containers': 'datalad containers-add --version'}
+    what_versions = {
+        'datalad': 'datalad --version',
+        'git': 'git --version',
+        'git-annex': 'git-annex version',
+        'datalad_containers': 'datalad containers-add --version',
+    }
     for key in what_versions:
         the_command = what_versions[key]
         try:
-            proc = subprocess.run(the_command.split(' '),
-                                  stdout=subprocess.PIPE)
+            proc = subprocess.run(the_command.split(' '), stdout=subprocess.PIPE)
             proc.check_returncode()
             if key == 'git-annex':
                 temp = proc.stdout.decode('utf-8').split('\n')[0]
                 config['version'][key] = temp
             else:
-                config['version'][key] = \
-                    proc.stdout.decode('utf-8').replace('\n', '')
-        except:
+                config['version'][key] = proc.stdout.decode('utf-8').replace('\n', '')
+        except Exception:
             config['version'][key] = 'not_installed'
 
         yaml_file.write('  ' + key + ": '" + config['version'][key] + "'\n")