From 4a2d4ef151ac17282ff21330ef4a72728bdcf08d Mon Sep 17 00:00:00 2001 From: Jochem Smit Date: Thu, 25 Apr 2024 13:12:57 +0200 Subject: [PATCH 1/6] Update mkdocs.yml remove configuration page --- mkdocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 480a738..06f3399 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -19,7 +19,6 @@ nav: - install.md - Usage: - usage/loading.md - - usage/configuration.md - API Reference: reference/ watch: From e1b77899d3a5836cdf3ac11ffb8482c7d9ff583c Mon Sep 17 00:00:00 2001 From: Jochem Smit Date: Thu, 25 Apr 2024 13:13:34 +0200 Subject: [PATCH 2/6] Delete docs/usage/configuration.md --- docs/usage/configuration.md | 30 ------------------------------ 1 file changed, 30 deletions(-) delete mode 100644 docs/usage/configuration.md diff --git a/docs/usage/configuration.md b/docs/usage/configuration.md deleted file mode 100644 index 75ab9f1..0000000 --- a/docs/usage/configuration.md +++ /dev/null @@ -1,30 +0,0 @@ -# Configuration - -Default values for HDXMS Datasets configuration are stored as a .yaml file in `~/.hdxms_datasets/config.yaml`. -The values there can be modified to update default settings. - -The default configuration is as follows: - -```yaml -database_dir: $home/.hdxms_datasets/datasets -database_url: https://raw.githubusercontent.com/Jhsmit/HDX-MS-datasets/master/datasets/ -time_unit: s - -dynamx: - time_unit: min - -``` - -Here `time_unit` defines the time unit in returned datasets. The `time_unit` in the `dynamx` section sets the time unit -of the source datasets in the DynamX format. - -Configuration settings can also be changed from within python: - -```python -from hdxms_datasets import cfg - -cfg.time_unit = 'min' - -``` - -This will change the time unit to minutes for all datasets loaded from then on. \ No newline at end of file From 3db37494b97f1107491a0bd296db12a9a63e6ba7 Mon Sep 17 00:00:00 2001 From: Jochem Smit Date: Thu, 13 Jun 2024 10:43:29 +0200 Subject: [PATCH 3/6] Update README.md --- README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7d18793..091faf5 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,15 @@ $ pip install hdxms-datasets ```python +from pathlib import Path from hdxms_datasets import DataVault -vault = DataVault() +# local path the download datasets to + +cache_dir = Path('.cache') + +# create a vault with local cache dir, set `remote_url` to connect to a different database +vault = DataVault(cache_dir=cache_dir) # Download a specific HDX dataset vault.fetch_dataset("20221007_1530_SecA_Krishnamurthy") From a2506556e16242f699ff36c320d099da5bcf111e Mon Sep 17 00:00:00 2001 From: Jochem Smit Date: Thu, 13 Jun 2024 10:43:43 +0200 Subject: [PATCH 4/6] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 091faf5..08b9d4f 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,6 @@ from pathlib import Path from hdxms_datasets import DataVault # local path the download datasets to - cache_dir = Path('.cache') # create a vault with local cache dir, set `remote_url` to connect to a different database From ed06b83b79338f1b917f197c52e5bff0fe40946b Mon Sep 17 00:00:00 2001 From: Jochem Smit Date: Thu, 13 Jun 2024 10:45:08 +0200 Subject: [PATCH 5/6] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 08b9d4f..1105eca 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,11 @@ $ pip install hdxms-datasets ``` +### HDX-MS database + +Currently a beta test database is set up at: +https://github.com/Jhsmit/HDX-MS-datasets + ### Example code From b1836df85de90eae3448a9f6612f2b0effbb79d2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 26 Nov 2024 18:08:47 +0000 Subject: [PATCH 6/6] Bump urllib3 from 2.1.0 to 2.2.2 in /requirements Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.1.0 to 2.2.2. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.1.0...2.2.2) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- requirements/requirements-macOS-latest-3.10.txt | 2 +- requirements/requirements-macOS-latest-3.9.txt | 2 +- requirements/requirements-ubuntu-latest-3.10.txt | 2 +- requirements/requirements-ubuntu-latest-3.9.txt | 2 +- requirements/requirements-windows-latest-3.10.txt | 2 +- requirements/requirements-windows-latest-3.9.txt | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/requirements/requirements-macOS-latest-3.10.txt b/requirements/requirements-macOS-latest-3.10.txt index e6785ae..15579cc 100644 --- a/requirements/requirements-macOS-latest-3.10.txt +++ b/requirements/requirements-macOS-latest-3.10.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests diff --git a/requirements/requirements-macOS-latest-3.9.txt b/requirements/requirements-macOS-latest-3.9.txt index 3269571..fca33a7 100644 --- a/requirements/requirements-macOS-latest-3.9.txt +++ b/requirements/requirements-macOS-latest-3.9.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests diff --git a/requirements/requirements-ubuntu-latest-3.10.txt b/requirements/requirements-ubuntu-latest-3.10.txt index ab71574..0411b26 100644 --- a/requirements/requirements-ubuntu-latest-3.10.txt +++ b/requirements/requirements-ubuntu-latest-3.10.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests diff --git a/requirements/requirements-ubuntu-latest-3.9.txt b/requirements/requirements-ubuntu-latest-3.9.txt index 89b1ad3..dcded15 100644 --- a/requirements/requirements-ubuntu-latest-3.9.txt +++ b/requirements/requirements-ubuntu-latest-3.9.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests diff --git a/requirements/requirements-windows-latest-3.10.txt b/requirements/requirements-windows-latest-3.10.txt index 8a4e9c7..89bba22 100644 --- a/requirements/requirements-windows-latest-3.10.txt +++ b/requirements/requirements-windows-latest-3.10.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests diff --git a/requirements/requirements-windows-latest-3.9.txt b/requirements/requirements-windows-latest-3.9.txt index 23282ba..a2df54c 100644 --- a/requirements/requirements-windows-latest-3.9.txt +++ b/requirements/requirements-windows-latest-3.9.txt @@ -28,5 +28,5 @@ six==1.16.0 # via python-dateutil tzdata==2023.4 # via pandas -urllib3==2.1.0 +urllib3==2.2.2 # via requests