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 31, 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:
Latest release

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 31, 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-0.1.198.tar.gz (41.5 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-0.1.198-py3-none-any.whl (47.3 kB view details)

Uploaded Python 3

File details

Details for the file npc_lims-0.1.198.tar.gz.

File metadata

  • Download URL: npc_lims-0.1.198.tar.gz
  • Upload date:
  • Size: 41.5 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: uv/0.12.0 {"installer":{"name":"uv","version":"0.12.0","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-0.1.198.tar.gz
Algorithm Hash digest
SHA256 c22ae7bffe5c3ff900a53b1ba684f70c7cba842a7daa838d9a74b9257d1e2e75
MD5 2aba98b86dbc54d37329cc133da10ab5
BLAKE2b-256 2e3325aa8431cbc2e262478c8868f2f9939d155bca40f866bcdbc25b9a27fbd6

See more details on using hashes here.

File details

Details for the file npc_lims-0.1.198-py3-none-any.whl.

File metadata

  • Download URL: npc_lims-0.1.198-py3-none-any.whl
  • Upload date:
  • Size: 47.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: uv/0.12.0 {"installer":{"name":"uv","version":"0.12.0","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-0.1.198-py3-none-any.whl
Algorithm Hash digest
SHA256 7a52234898cbb0f4f9c65cfe84380c8f4969c0e15250a983b77d38e41e61a241
MD5 5589b7366794d2a7da5e44a89e5cc473
BLAKE2b-256 c25a7b93ec11f7c0cff77d7455e9b29d8b928749676e34b7f1d159073f11f490

See more details on using hashes here.

Release history Release notifications | RSS feed

This release

0.1.198 This release

2 files

0.1.197

2 files

0.1.196

2 files

0.1.195

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