build: major dependencies update

.github/workflows/docs.yml

@@ -2,7 +2,7 @@ name: docs
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, upgrade_ci]
   workflow_dispatch:
 
 jobs:
@@ -15,25 +15,26 @@ jobs:
 
     steps:
       - name: check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: set up Conda/Mamba
-        uses: conda-incubator/setup-miniconda@v2
+      - name: set up Miniforge with ZARP-cli environment
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: "3.10"
-          mamba-version: "*"
+          environment-file: install/environment.dev.yml
+          miniforge-version: latest
+          conda-remove-defaults: true
+          channel-priority: strict
           auto-update-conda: true
-          activate-environment: zarp-cli
-          environment-file: install/environment.dev.root.yml
           auto-activate-base: false
+          activate-environment: zarp-cli
 
-      - name: display environment info
+      - name: display Conda and environment info
         run: |
           conda info -a
           conda list
 
       - name: cache build artifacts
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           key: ${{ github.ref }}
           path: .cache

.github/workflows/tests.yml

@@ -12,23 +12,29 @@ jobs:
 
     steps:
       - name: check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: set up Conda/Mamba
-        uses: conda-incubator/setup-miniconda@v2
+      - name: set up Miniforge with ZARP-cli environment
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: "3.10"
-          mamba-version: "*"
-          auto-update-conda: true
-          activate-environment: zarp-cli
           environment-file: install/environment.dev.yml
+          miniforge-version: latest
+          conda-remove-defaults: true
+          channel-priority: strict
+          auto-update-conda: true
           auto-activate-base: false
+          activate-environment: zarp-cli
 
-      - name: display environment info
+      - name: display Conda and environment info
         run: |
           conda info -a
           conda list
 
+      - name: Install Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6
+
       - name: flake8
         run: flake8
 
@@ -43,31 +49,32 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [ '3.9', '3.10' ]
-    name: unit-testing-Python-${{ matrix.python-version }}
 
     steps:
       - name: check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: set up Conda/Mamba
-        uses: conda-incubator/setup-miniconda@v2
+      - name: set up Miniforge with ZARP-cli environment
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
+          environment-file: install/environment.dev.yml
+          miniforge-version: latest
+          conda-remove-defaults: true
+          channel-priority: strict
           auto-update-conda: true
-          activate-environment: zarp-cli
-          environment-file: install/environment.dev.root.yml
           auto-activate-base: false
+          activate-environment: zarp-cli
 
-      - name: display environment info
+      - name: display Conda and environment info
         run: |
           conda info -a
           conda list
 
+      - name: Install Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+          apptainer-version: 1.3.6
+
       - name: run unit tests
         run: |
           coverage run --source zarp -m pytest && coverage xml
@@ -85,27 +92,23 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: [ '3.9', '3.10' ]
-    name: integration-testing-Python-${{ matrix.python-version }}
 
     steps:
       - name: check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: set up Conda/Mamba
-        uses: conda-incubator/setup-miniconda@v2
+      - name: set up Miniforge with ZARP-cli environment
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
+          environment-file: install/environment.dev.yml
+          miniforge-version: latest
+          conda-remove-defaults: true
+          channel-priority: strict
           auto-update-conda: true
-          activate-environment: zarp-cli
-          environment-file: install/environment.dev.root.yml
           auto-activate-base: false
+          activate-environment: zarp-cli
 
-      - name: display environment info
+      - name: display Conda and environment info
         run: |
           conda info -a
           conda list

docs/guides/initialization.md

@@ -41,7 +41,7 @@ The following configuration options are available.
 | `zarp_directory` | Path to the local copy of the [ZARP workflow repository][zarp] | `../zarp` relative to the location of the ZARP-cli repository |
 | `execution_mode` | Trigger a full _ZARP-cli_ run (`RUN`), a dry run (`DRY_RUN`; external tools are not actually run, only logs what _would be_ run; useful for testing) or prepare a _ZARP_ run (`PREPARE_RUN`; _ZARP-cli_ is run normally, including all external tools, up until the point of the execution of the actual _ZARP_ workflow; use to manually check metadata table before _ZARP_ execution)  | `RUN` |
 | `cores` | Number of CPU cores that Snakemake is run with when executing _ZARP_ and the auxiliary workflows (fetching libraries from [SRA][sra], inferring metadata) | `1` |
-| `dependency_embedding` | Whether Snakemake should use `CONDA` or containers (`SINGULARITY`) to manage dependencies of each workflow step/rule | `CONDA` |
+| `dependency_embedding` | Whether Snakemake should use `CONDA` or containers (`APPTAINER`) to manage dependencies of each workflow step/rule | `CONDA` |
 | `genome_assemblies_map` | A headerless 3-column semicolon-separated mapping table of organism/source trivial names (e.g., `homo_sapiens`), optional comma-separated aliases such as NCBI taxon IDs and/or organism/source short names (e.g., `7227,dmelanogaster`) and a corresponding genome assembly name (e.g., `GRCm39`); a table in the required format is shipped with _ZARP_cli_ in the the default location; it can be amended with additional aliases; note that for [`genomepy`][genomepy] to be able to pull genome annotations for organisms/sources that [HTSinfer][htsinfer] inferred, NCBI taxon ID aliases are _required_  | `./data/genome_assemblies.csv` relative to the location of the ZARP-cli repository |
 | `resources_version` | Whether to always download the latest available version of genome annotations for a given organism/source from Ensembl (enter `None`; default) or whether to use a specific version of the corresponding Ensembl database (e.g., `100`); note that the different Ensembl databases (e.g., for fungi, plants) use a different versioning scheme, so pinning a particular database version may lead to unexpected outcomes | `None` |
 | `rule_config` | A configuration file for the _ZARP_ workflow that sets specific parameters for each workflow step ("rule"); see [ZARP][zarp] documentation for details | `None` |

docs/guides/installation.md

@@ -9,7 +9,7 @@ Installation requires the following:
 - Linux (tested with Ubuntu 20.04; macOS has not been tested yet)
 - [Conda][conda] (tested with `conda 22.11.1`)
 - [Mamba][mamba] (tested with `mamba 1.3.0`)
-- [Singularity][singularity] (tested with `singularity 3.8.6`; not required
+- [Apptainer][apptainer] (tested with `apptainer 1.3.6`; not required
   if you have root permissions on the machine you would like to install
   _ZARP-cli_ on; in that case, choose one of the `.root.` environment file
   flavors [below](#3-set-up-environment))

docs/includes/references.md

@@ -1,3 +1,4 @@
+[apptainer]: <https://apptainer.org/>
 [bioanalyzer]: <https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems>
 [conda]: <https://docs.conda.io/projects/conda/en/latest/index.html>
 [contact]: <mailto:zavolab-biozentrum@unibas.ch>
@@ -9,7 +10,6 @@
 [kallisto]: <https://github.com/pachterlab/kallisto>
 [mamba]: <https://github.com/mamba-org/mamba>
 [salmon]: <https://github.com/COMBINE-lab/salmon>
-[singularity]: <https://sylabs.io/singularity/>
 [snakemake]: <https://github.com/snakemake/snakemake>
 [snakemake-profiles]: <https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles>
 [sra]: <https://www.ncbi.nlm.nih.gov/sra>
@@ -21,4 +21,4 @@
 [zarp-qa]: <https://github.com/zavolanlab/zarp/discussions>
 [zarp-supplementary]: <https://zenodo.org/records/10797372.
 [zavolab-gh]: <https://github.com/zavolanlab>
-[zenodo]: <https://zenodo.org/>
+[zenodo]: <https://zenodo.org/>

install/environment.dev.yml

@@ -1,17 +1,14 @@
 name: zarp-cli
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
 dependencies:
+  - bioconda::genomepy >=0.15.0
+  - bioconda::snakemake >=8
   - addict >=2.4.0
   - bidict >=0.22.0
   - black >=20.8b1
   - coverage>=5.4
   - email-validator >=1.2.1
   - flake8>=3.8.4
   - flake8-docstrings >=1.6.0
-  - genomepy >=0.15.0
   - jsonref >=0.2
   - mypy >=0.812
   - numpy >=1.22, <1.25
@@ -22,11 +19,10 @@ dependencies:
   - pygments >=2.8.0
   - pylint >=2.7.1
   - pytest >=6.2.2
-  - python >=3.9, <=3.10
+  - python >=3.11
   - python-semantic-release >=7.15.0
   - rich >=12.5.1
-  - snakemake >=7.19.1
-  - types-PyYAML >=6.0.11
+  - types-pyyaml >=6.0.11
   - pip:
     - -e ..
 

install/environment.yml

@@ -1,21 +1,17 @@
 name: zarp-cli
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
 dependencies:
+  - biconda::genomepy >=0.15.0
+  - bioconda::snakemake >=8
   - addict >=2.4.0
   - bidict >=0.22.0
   - email-validator >=1.2.1
-  - genomepy >=0.15.0
   - jsonref >=0.2
   - numpy >=1.22, <1.25
   - pandas >=1.3.5, <1.4.0
   - pip >=22.1
   - pydantic >=1.9.2, <2.0.0
   - pygments >=2.8.0
-  - python >=3.9, <=3.10
+  - python >=3.11
   - rich >=12.5.1
-  - snakemake >=7.19.1
   - pip:
     - -e ..

setup.py

@@ -1,4 +1,4 @@
-"""ZARP CLI package definition."""
+"""ZARP-cli package definition."""
 
 from pathlib import Path
 
@@ -32,8 +32,7 @@
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: Apache Software License",
         "Natural Language :: English",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Utilities",
     ],

tests/config/test_args.py

@@ -123,7 +123,7 @@ def test_process_arguments_execution_mode(self, test_input):
 
     @pytest.mark.parametrize(
         "test_input",
-        ["CONDA", "SINGULARITY"],
+        ["CONDA", "APPTAINER"],
     )
     def test_process_arguments_dependency_embedding(self, test_input):
         """Test method ``.process_arguments()``.

tests/snakemake/test_run.py

@@ -63,7 +63,7 @@ def test_compile_command_config_file(self, tmpdir):
         config_file = create_config_file(dir=Path(tmpdir))
         run_config = default_run_config.copy(deep=True)
         run_config.dependency_embedding = (
-            DependencyEmbeddingStrategies.SINGULARITY
+            DependencyEmbeddingStrategies.APPTAINER
         )
         my_run = SnakemakeExecutor(
             run_config=run_config,
@@ -92,7 +92,7 @@ def test_compile_command_profile(self, tmpdir):
         "dependency_embedding",
         [
             DependencyEmbeddingStrategies.CONDA,
-            DependencyEmbeddingStrategies.SINGULARITY,
+            DependencyEmbeddingStrategies.APPTAINER,
         ],
     )
     def test_compile_command_dep_embedding(self, dependency_embedding, tmpdir):

zarp/config/enums.py

@@ -10,11 +10,11 @@ class DependencyEmbeddingStrategies(Enum):
 
     Attributes:
         CONDA: Use binaries from Conda.
-        SINGULARITY: Use Singularity containers.
+        APPTAINER: Use Apptainer (formerly Singularity) containers.
     """
 
     CONDA = "CONDA"
-    SINGULARITY = "SINGULARITY"
+    APPTAINER = "APPTAINER"
 
 
 class ExecModes(Enum):