initial commit after cleanup

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# PyCharm project settings
+.idea
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Data folders

README.md

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+# paper-brain-wide-map
+Code related to the brainwide map paper
+
+
+# Installation
+## Create a new python environment (optional)
+
+Install [Anaconda](https://www.anaconda.com/distribution/#download-section) and [git](https://git-scm.com/downloads), 
+and follow their installer instructions to add each to the system path
+
+Create new python environment
+```
+conda create --name ibl_bwm python=3.9
+```
+Activate environment
+```
+conda activate ibl_bwm
+```
+
+## Download and Install repository
+
+Clone the repo 
+```
+git clone https://github.com/int-brain-lab/paper-brain-wide-map.git
+```
+
+Navigate to repo
+```
+cd paper-brain-wide-map
+```
+
+Install requirements and repo
+```
+pip install -e .
+```
+
+## Query sessions for BWM analyses
+You can now use the following in Python (note that ONE needs to be set up)
+```python
+from brainwidemap import bwm_query
+from one.api import ONE
+
+one = ONE()
+bwm_df = bwm_query(one)
+```

brainwidemap/__init__.py

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+from brainwidemap.bwm_loading import bwm_query
+
+__version__ = "0.0.1"

brainwidemap/bwm_loading.py

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+from dateutil import parser
+import numpy as np
+import pandas as pd
+
+
+def bwm_query(one, alignment_resolved=True, return_details=False):
+    """
+    Function to query for brainwide map sessions that pass the most important quality controls. Returns a dataframe
+    with one row per insertions and columns ['pid', 'eid', 'probe_name', 'session_number', 'date', 'subject', 'lab']
+
+    Parameters
+    ----------
+    one: ONE instance (can be remote or local)
+    alignment_resolved: bool, default is True. If True, only returns sessions with resolved alignment,
+                        if False returns all sessions with at least one alignment
+    return_details: bool, default is False. If True returns a second output a list containing the full insertion
+                    dictionary for all insertions returned by the query. Only needed if you need information that is
+                    not contained in the output dataframe
+
+    Returns
+    -------
+    bwm_df: pd.DataFrame of BWM sessions to be included in analyses with columns
+            ['pid', 'eid', 'probe_name', 'session_number', 'date', 'subject', 'lab']
+    """
+
+    base_query = (
+        'session__project__name__icontains,ibl_neuropixel_brainwide_01,'
+        'session__json__IS_MOCK,False,'
+        'session__qc__lt,50,'
+        '~json__qc,CRITICAL,'
+        'session__extended_qc__behavior,1,'
+        'json__extended_qc__tracing_exists,True,'
+    )
+
+    if alignment_resolved:
+        base_query += 'json__extended_qc__alignment_resolved,True,'
+    else:
+        base_query += 'json__extended_qc__alignment_count__gt,0,'
+
+    qc_pass = (
+        '~session__extended_qc___task_stimOn_goCue_delays__lt,0.9,'
+        '~session__extended_qc___task_response_feedback_delays__lt,0.9,'
+        '~session__extended_qc___task_wheel_move_before_feedback__lt,0.9,'
+        '~session__extended_qc___task_wheel_freeze_during_quiescence__lt,0.9,'
+        '~session__extended_qc___task_error_trial_event_sequence__lt,0.9,'
+        '~session__extended_qc___task_correct_trial_event_sequence__lt,0.9,'
+        '~session__extended_qc___task_reward_volumes__lt,0.9,'
+        '~session__extended_qc___task_reward_volume_set__lt,0.9,'
+        '~session__extended_qc___task_stimulus_move_before_goCue__lt,0.9,'
+        '~session__extended_qc___task_audio_pre_trial__lt,0.9')
+
+    marked_pass = (
+        'session__extended_qc___experimenter_task,PASS')
+
+    insertions = list(one.alyx.rest('insertions', 'list', django=base_query + qc_pass))
+    insertions.extend(list(one.alyx.rest('insertions', 'list', django=base_query + marked_pass)))
+
+    bwm_df = pd.DataFrame({
+        'pid': np.array([i['id'] for i in insertions]),
+        'eid': np.array([i['session'] for i in insertions]),
+        'probe_name': np.array([i['name'] for i in insertions]),
+        'session_number': np.array([i['session_info']['number'] for i in insertions]),
+        'date': np.array([parser.parse(i['session_info']['start_time']).date() for i in insertions]),
+        'subject': np.array([i['session_info']['subject'] for i in insertions]),
+        'lab': np.array([i['session_info']['lab'] for i in insertions]),
+    }).sort_values(by=['lab', 'subject', 'date', 'eid'])
+    bwm_df.drop_duplicates(inplace=True)
+    bwm_df.reset_index(inplace=True, drop=True)
+
+    if return_details:
+        return bwm_df, insertions
+    else:
+        return bwm_df

requirements.txt

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+ONE-api
+ibllib
+numpy
+pandas
+python-dateutil

setup.py

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+from setuptools import setup, find_packages
+import sys
+from pathlib import Path
+
+CURRENT_DIRECTORY = Path(__file__).parent.absolute()
+
+CURRENT_PYTHON = sys.version_info[:2]
+REQUIRED_PYTHON = (3, 8)
+if CURRENT_PYTHON < REQUIRED_PYTHON:
+    sys.stderr.write("""
+==========================
+Unsupported Python version
+==========================
+This version of iblutil requires Python {}.{}, but you're trying to
+install it on Python {}.{}.
+""".format(*(REQUIRED_PYTHON + CURRENT_PYTHON)))
+    sys.exit(1)
+
+with open("README.md", 'r') as f:
+    long_description = f.read()
+
+with open('requirements.txt') as f:
+    require = [x.strip() for x in f.readlines() if not x.startswith('git+')]
+
+setup(
+    name='brainwidemap',
+    version='0.1.0',
+    python_requires='>={}.{}'.format(*REQUIRED_PYTHON),
+    description='Github repo for code associated with IBL brainwide map paper',
+    license="MIT",
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    author='IBL',
+    url="https://www.internationalbrainlab.com/",
+    packages=find_packages(exclude=['scratch', 'tests']),  # same as name
+    include_package_data=True,
+    # external packages as dependencies
+    install_requires=require,
+    entry_points={},
+    scripts={}
+)