From 83b51dc15a93e7d6d47a7e7ceaa77de25069cb2d Mon Sep 17 00:00:00 2001 From: Myles Verdon Date: Mon, 11 Aug 2025 15:22:22 +0100 Subject: [PATCH 1/3] feat: added deprecation warnings --- docs/intro.md | 6 ++++++ src/pathogena/cli.py | 5 ++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/intro.md b/docs/intro.md index 27d60b2..57e1856 100644 --- a/docs/intro.md +++ b/docs/intro.md @@ -1,3 +1,9 @@ +> # ⚠️ Deprecated +> +> `pathogena` has been renamed `gpas`. Please use the [GPAS PyPI project](https://pypi.org/project/gpas/) instead. +> +> The package under this name will no longer be receiving updates. + # EIT Pathogena Client The command line interface for the EIT Pathogena platform. diff --git a/src/pathogena/cli.py b/src/pathogena/cli.py index 3c2f018..180040e 100644 --- a/src/pathogena/cli.py +++ b/src/pathogena/cli.py @@ -20,7 +20,10 @@ ) def main(*, debug: bool = False) -> None: """EIT Pathogena command line interface.""" - lib.check_for_newer_version() + logging.warning( + f"⚠️ Deprecated! ⚠️ \n'pathogena' has been renamed to 'gpas' - please use https://pypi.org/project/gpas/. \n" + f"The package under this name will no longer be receiving updates." + ) util.display_cli_version() configure_debug_logging(debug) From 4ef77b70cb96a0d2003dd995668d11cbbb3aed03 Mon Sep 17 00:00:00 2001 From: Myles Verdon Date: Mon, 11 Aug 2025 15:32:05 +0100 Subject: [PATCH 2/3] feat: update version and readme --- CHANGELOG.md | 4 +++- Dockerfile | 2 +- README_pypi.md | 12 +++++++++--- src/pathogena/__init__.py | 2 +- 4 files changed, 14 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b2d3e53..1c5dd7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,6 @@ -## Unreleased +## 2.2.2 + +- Deprecate ## 2.2.1 (2025-07-03) diff --git a/Dockerfile b/Dockerfile index 9b280ad..cc6e41c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Bioconda-based build against latest PyPI release # Created for a specific user. Not part of the pypi release process FROM condaforge/miniforge3:latest -ENV PATHOGENA_CLIENT_VERSION=2.2.1 +ENV PATHOGENA_CLIENT_VERSION=2.2.2 RUN mamba install -c bioconda hostile==1.1.0 RUN pip install https://pypi.io/packages/source/g/pathogena/pathogena-${PATHOGENA_CLIENT_VERSION}.tar.gz diff --git a/README_pypi.md b/README_pypi.md index e01e6ff..9b310bc 100644 --- a/README_pypi.md +++ b/README_pypi.md @@ -1,3 +1,9 @@ +> # ⚠️ Deprecated +> +> `pathogena` has been renamed `gpas`. Please use the [GPAS PyPI project](https://pypi.org/project/gpas/) instead. +> +> The package under this name will no longer be receiving updates. + # EIT Pathogena Client The command line interface for the EIT Pathogena platform. @@ -303,7 +309,7 @@ Options: --output-csv FILE Path to output CSV file [required] --batch-name TEXT Batch name [required] --collection-date [%Y-%m-%d] Collection date (YYYY-MM-DD) [default: - 2025-07-03; required] + 2025-08-11; required] --country TEXT 3-letter Country Code [required] --instrument-platform [illumina|ont] Sequencing technology @@ -324,7 +330,7 @@ Options: -h, --help Show this message and exit. ``` -This command generates a CSV from a given directory of fastq sample files. An [example](https://github.com/EIT-Pathogena/client/tree/2.2.1/docs/assets) of such a CSV file is given in the assets directory. A CSV file in this format is required to run the [pathogena upload](#pathogena-upload) command. +This command generates a CSV from a given directory of fastq sample files. An [example](https://github.com/EIT-Pathogena/client/tree/2.2.2/docs/assets) of such a CSV file is given in the assets directory. A CSV file in this format is required to run the [pathogena upload](#pathogena-upload) command. Note: the CSV file must be located in the same directory as the sample.fastq files to be used with the upload command. @@ -373,7 +379,7 @@ Options: ``` This command will attempt to remove human reads from a given input CSV file, in the same structure as the input CSV that -would be used for uploading to EIT Pathogena, an [example can be found here](https://github.com/EIT-Pathogena/client/tree/2.2.1/docs/assets). +would be used for uploading to EIT Pathogena, an [example can be found here](https://github.com/EIT-Pathogena/client/tree/2.2.2/docs/assets). By default, the processed files will be output in the same directory that the command is run in, but you can choose a different directory with the `--output-dir` argument. diff --git a/src/pathogena/__init__.py b/src/pathogena/__init__.py index 3e88a3c..fa559f7 100644 --- a/src/pathogena/__init__.py +++ b/src/pathogena/__init__.py @@ -1,3 +1,3 @@ """The command line and Python client for EIT Pathogena.""" -__version__ = "2.2.1" +__version__ = "2.2.2" From 0e5afc34209b54efb4bb5ac262b65c18b41c4de8 Mon Sep 17 00:00:00 2001 From: Myles Verdon Date: Mon, 18 Aug 2025 17:26:00 +0100 Subject: [PATCH 3/3] build: 2.2.2rc1 --- CHANGELOG.md | 4 ++-- Dockerfile | 2 +- src/pathogena/__init__.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c5dd7f..9b31056 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ -## 2.2.2 +## 2.2.2rc1 (2025-08-18) -- Deprecate +- [EV-2285](https://eit-oxford.atlassian.net/browse/EV-2285) Add deprecation warnings to client ## 2.2.1 (2025-07-03) diff --git a/Dockerfile b/Dockerfile index cc6e41c..98a2c88 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Bioconda-based build against latest PyPI release # Created for a specific user. Not part of the pypi release process FROM condaforge/miniforge3:latest -ENV PATHOGENA_CLIENT_VERSION=2.2.2 +ENV PATHOGENA_CLIENT_VERSION=2.2.2rc1 RUN mamba install -c bioconda hostile==1.1.0 RUN pip install https://pypi.io/packages/source/g/pathogena/pathogena-${PATHOGENA_CLIENT_VERSION}.tar.gz diff --git a/src/pathogena/__init__.py b/src/pathogena/__init__.py index fa559f7..4ffaeb0 100644 --- a/src/pathogena/__init__.py +++ b/src/pathogena/__init__.py @@ -1,3 +1,3 @@ """The command line and Python client for EIT Pathogena.""" -__version__ = "2.2.2" +__version__ = "2.2.2rc1"