diff --git a/.github/workflows/conda-build.yml b/.github/workflows/conda-build.yml index 03b2337..5819a95 100644 --- a/.github/workflows/conda-build.yml +++ b/.github/workflows/conda-build.yml @@ -4,9 +4,11 @@ on: push: branches: - master + - dev pull_request: branches: - master + - dev jobs: build: @@ -20,50 +22,31 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true - python-version: 3.8 + python-version: 3.12 channels: conda-forge,defaults,bioconda - - name: Create conda environment - run: conda env create -f environment.yml - - name: Install mamba, boa and conda-build run: | source $CONDA/etc/profile.d/conda.sh - conda activate pridepy - conda install conda-forge::mamba - conda install conda-forge::boa - mamba install conda-build anaconda-client + conda install conda-forge::mamba conda-forge::boa conda-forge::conda-build anaconda-client shell: bash -l {0} - - name: Activate conda environment and build package + - name: Build package run: | source $CONDA/etc/profile.d/conda.sh - conda activate pridepy conda mambabuild recipe - shell: bash -l {0} - - - name: Install the built package - run: | - source $CONDA/etc/profile.d/conda.sh - conda activate pridepy mamba install --use-local pridepy - shell: bash -l {0} - - - name: Output package info - run: | - source $CONDA/etc/profile.d/conda.sh - conda activate pridepy - conda list + pridepy --help shell: bash -l {0} - name: Test the installed package run: | - conda activate pridepy + source $CONDA/etc/profile.d/conda.sh pridepy --help shell: bash -l {0} - name: Test download file with aspera from conda run: | - conda activate pridepy + source $CONDA/etc/profile.d/conda.sh pridepy download-file-by-name -a PXD022105 -o ./ -f checksum.txt -p aspera shell: bash -l {0} \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md index 68ad298..2575bfa 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -81,7 +81,7 @@ For small files (~14MB), the three have similar performance. For medium (~230MB) # Discussion and Future Directions -`pridepy` (https://github.com/PRIDE-Archive/pridepy) successfully simplifies access to the PRIDE Archive data, but future development could focus on improving the handling of large downloads by implementing parallel downloads. Additionally, we will expand the user documentation and examples could help broaden its use within the scientific community; and at the same time produce a group of benchmarks to evaluate the performance of the client in different scenarios. We plat to continue extending the library to support more features of the PRIDE Archive API, such as dataset metadata streaming, and submission of new datasets to the PRIDE Archive. +`pridepy` (https://github.com/PRIDE-Archive/pridepy) successfully simplifies access to the PRIDE Archive data, but future development could focus on improving the handling of large downloads by implementing parallel downloads. Additionally, we will expand the user documentation and examples could help broaden its use within the scientific community; and at the same time produce a group of benchmarks to evaluate the performance of the client in different scenarios. We are working to implement downloads using Globus protocol using the Globus client and not the https of the EBI Globus collection. We plan to continue extending the library to support more features of the PRIDE Archive API, such as dataset metadata streaming, and submission of new datasets to the PRIDE Archive. # Acknowledgments diff --git a/paper/paper.pdf b/paper/paper.pdf index a7edcfa..7181135 100644 Binary files a/paper/paper.pdf and b/paper/paper.pdf differ diff --git a/recipe/meta.yaml b/recipe/meta.yaml index f20cd15..a68610a 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -17,8 +17,9 @@ build: requirements: host: - - python >=3.8,<4.0 + - python >=3.9 - pip + - setuptools run: - requests~=2.31.0 - ratelimit~=2.2.1 @@ -29,6 +30,7 @@ requirements: - boto3~=1.34.61 - botocore~=1.34.74 - tqdm + - httpx test: imports: diff --git a/setup.py b/setup.py index 171aa15..b711be1 100644 --- a/setup.py +++ b/setup.py @@ -26,6 +26,7 @@ "tqdm", "boto3", "botocore", + "httpx", ], include_package_data=True, package_data={