fix the conda build.

.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}

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
 

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:

setup.py

@@ -26,6 +26,7 @@
         "tqdm",
         "boto3",
         "botocore",
+        "httpx",
     ],
     include_package_data=True,
     package_data={