npc_lims

neuropixels cloud lab information management system Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.

PyPI Python version

Coverage CI/CD GitHub issues

quickstart

  • make a new Python >=3.9 virtual environment with conda or venv (lighter option, since this package does not require pandas, numpy etc.):

    python -m venv .venv

  • activate the virtual environment:

    • Windows
    .venv\scripts\activate
    • Unix
    source .venv/bin/activate.sh

  • install the package:

    python -m pip install npc_lims

  • setup credentials

    • required environment variables:
      • AWS S3
        • AWS_DEFAULT_REGION
        • AWS_ACCESS_KEY_ID
        • AWS_SECRET_ACCESS_KEY
        • to find and read files on S3
        • must have read access on relevant aind buckets
        • can be in a standard ~/.aws location, as used by AWS CLI or boto3
      • CodeOcean API
        • CODE_OCEAN_API_TOKEN
        • CODE_OCEAN_DOMAIN
        • to find processed data in "data assets" via the Codeocean API
        • generated in CodeOcean:
          • right click on Account (bottom left, person icon)
          • click User Secrets - these are secrets than can be made available as environment variables in CodeOcean capsules
          • go to Access Tokens and click Generate new token - this is for programatically querying CodeOcean's databases
            • in Token Name enter Codeocean API (read) and check read on capsules and datasets
            • a token will be generated: click copy (storing it in a password manager, if you use one)
          • head back to User Secrets where we'll paste it into a new secret via Add secret > API credentials - in description enter Codeocean API (read) - in API key enter CODE_OCEAN_API_KEY - in API secret paste the copied secret from before (should start with cop_...) CODE_OCEAN_DOMAIN is the codeocean https address, up to and including .org
    • environment variables can also be specified in a file named .env in the current working directory

  • now in Python we can find sessions that are available to work with:

        >>> import npc_lims;

# get a sequence of `SessionInfo` dataclass instances, one per session:
    >>> tracked_sessions: tuple[npc_lims.SessionInfo, ...] = npc_lims.get_session_info()

# each `SessionInfo` instance has minimal metadata about its session:
    >>> tracked_sessions[0]                 # doctest: +SKIP
    npc_lims.SessionInfo(id='626791_2022-08-15', subject=626791, date='2022-08-15', idx=0, project='DRPilotSession', is_ephys=True, is_sync=True, allen_path=PosixUPath('//allen/programs/mindscope/workgroups/dynamicrouting/PilotEphys/Task 2 pilot/DRpilot_626791_20220815'))
        >>> tracked_sessions[0].is_ephys        # doctest: +SKIP
    False

# currently, we're only tracking behavior and ephys sessions that use variants of https://github.com/samgale/DynamicRoutingTask/blob/main/TaskControl.py:
    >>> all(s.date.year >= 2022 for s in tracked_sessions)
    True

  • "tracked sessions" are discovered via 3 routes:

Project links

Data verified by PyPI on Jul 20, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (0.1.198)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for bjhardcastle from gravatar.com bjhardcastle

Credits

Author: Arjun Sridhar

GitHub Statistics

Data verified by PyPI on Jul 20, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python >=3.9

Provides Extra

polars

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

npc_lims-0.1.195.tar.gz (40.8 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

npc_lims-0.1.195-py3-none-any.whl (47.1 kB view details)

Uploaded Python 3

File details

Details for the file npc_lims-0.1.195.tar.gz.

File metadata

  • Download URL: npc_lims-0.1.195.tar.gz
  • Upload date:
  • Size: 40.8 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: uv/0.11.30 {"installer":{"name":"uv","version":"0.11.30","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}

File hashes

Hashes for npc_lims-0.1.195.tar.gz
Algorithm Hash digest
SHA256 a7ebd3dfe1a2f09120021aa69de7f851a17e17029d25570c3f775d9c742d78f1
MD5 27d5be14a5e24f3dca862a679fea7da6
BLAKE2b-256 7f6106c506190057dbdfc33159a103841a9800963b89c49d86406d8a653bed6d

See more details on using hashes here.

File details

Details for the file npc_lims-0.1.195-py3-none-any.whl.

File metadata

  • Download URL: npc_lims-0.1.195-py3-none-any.whl
  • Upload date:
  • Size: 47.1 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: uv/0.11.30 {"installer":{"name":"uv","version":"0.11.30","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}

File hashes

Hashes for npc_lims-0.1.195-py3-none-any.whl
Algorithm Hash digest
SHA256 8bc16e00d4808319b58afffbacf8286e997afd4ea011032ddc9b91bfcfe50f51
MD5 6f10ae1b26051e3711f4c9faffc44c84
BLAKE2b-256 cde45e29e404311279a978b1baee49e824a98087d0effdb91edf2d4e3274cb4a

See more details on using hashes here.

Release history Release notifications | RSS feed

0.1.198

2 files

0.1.197

2 files

0.1.196

2 files

This release

0.1.195 This release

2 files

0.1.194

2 files

0.1.193

2 files

0.1.192

2 files

0.1.191

2 files

0.1.190

2 files

0.1.189

2 files

0.1.188

2 files

0.1.187

2 files

0.1.186

2 files

0.1.185

2 files

0.1.184

2 files

0.1.183

2 files

0.1.182

2 files

0.1.181

2 files

0.1.180

2 files

0.1.179

2 files

0.1.178

2 files

0.1.177

2 files

0.1.176

2 files

0.1.175

2 files

0.1.174

2 files

0.1.173

2 files

0.1.172

2 files

0.1.171

2 files

0.1.170

2 files

0.1.169

2 files

0.1.168

2 files

0.1.167

2 files

0.1.166

2 files

0.1.165

2 files

0.1.164

2 files

0.1.163

2 files

0.1.162

2 files

0.1.161

2 files

0.1.160

2 files

0.1.159

2 files

0.1.158

2 files

0.1.157

2 files

0.1.156

2 files

0.1.155

2 files

0.1.154

2 files

0.1.153

2 files

0.1.152

2 files

0.1.151

2 files

0.1.150

2 files

0.1.149

2 files

0.1.148

2 files

0.1.147

2 files

0.1.146

2 files

0.1.145

2 files

0.1.144

2 files

0.1.143

2 files

0.1.142

2 files

0.1.141

2 files

0.1.140

2 files

0.1.139

2 files

0.1.138

2 files

0.1.137

2 files

0.1.136

2 files

0.1.135

2 files

0.1.134

2 files

0.1.133

2 files

0.1.132

2 files

0.1.131

2 files

0.1.130

2 files

0.1.129

2 files

0.1.128

2 files

0.1.127

2 files

0.1.126

2 files

0.1.125

2 files

0.1.124

2 files

0.1.123

1 file

0.1.122

2 files

0.1.121

1 file

0.1.120

2 files

0.1.119

2 files

0.1.118

2 files

0.1.117

2 files

0.1.116

2 files

0.1.115

2 files

0.1.114

2 files

0.1.113

2 files

0.1.112

2 files

0.1.111

2 files

0.1.110

2 files

0.1.109

2 files

0.1.108

2 files

0.1.107

2 files

0.1.106

2 files

0.1.105

2 files

0.1.104

2 files

0.1.103

2 files

0.1.102

2 files

0.1.101

2 files

0.1.100

2 files

0.1.99

2 files

0.1.98

2 files

0.1.97

2 files

0.1.96

2 files

0.1.95

2 files

0.1.94

2 files

0.1.93

2 files

0.1.92

2 files

0.1.91

2 files

0.1.90

2 files

0.1.89

2 files

0.1.88

2 files

0.1.87

2 files

0.1.86

2 files

0.1.85

2 files

0.1.84

2 files

0.1.83

2 files

0.1.82

2 files

0.1.81

2 files

0.1.80

2 files

0.1.79

2 files

0.1.78

2 files

0.1.77

2 files

0.1.76

2 files

0.1.75

2 files

0.1.74

2 files

0.1.73

2 files

0.1.72

2 files

0.1.71

2 files

0.1.70

2 files

0.1.69

2 files

0.1.68

2 files

0.1.67

2 files

0.1.66

2 files

0.1.65

2 files

0.1.64

2 files

0.1.63

2 files

0.1.62

2 files

0.1.61

2 files

0.1.60

2 files

0.1.59

2 files

0.1.58

2 files

0.1.57

2 files

0.1.56

2 files

0.1.55

2 files

0.1.54

2 files

0.1.53

2 files

0.1.52

2 files

0.1.51

2 files

0.1.50

2 files

0.1.49

2 files

0.1.48

2 files

0.1.47

2 files

0.1.46

2 files

0.1.45

2 files

0.1.44

2 files

0.1.43

2 files

0.1.42

2 files

0.1.41

2 files

0.1.40

2 files

0.1.39

2 files

0.1.38

2 files

0.1.37

2 files

0.1.36

2 files

0.1.35

2 files

0.1.34

2 files

0.1.33

2 files

0.1.32

2 files

0.1.31

2 files

0.1.30

2 files

0.1.29

2 files

0.1.28

2 files

0.1.27

2 files

0.1.26

2 files

0.1.25

2 files

0.1.24

2 files

0.1.23

2 files

0.1.22

2 files

0.1.21

2 files

0.1.20

2 files

0.1.19

2 files

0.1.18

2 files

0.1.17

2 files

0.1.16

2 files

0.1.15

2 files

0.1.14

2 files

0.1.13

2 files

0.1.12

2 files

0.1.11

2 files

0.1.10

2 files

0.1.9

2 files

0.1.8

2 files

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page