Merge pull request #48 from iqbal-lab-org/fix/remove_pip

fix: remove poetry infrastructure and update integration tests and CI

.github/workflows/ci.yaml

@@ -32,7 +32,7 @@ jobs:
             python=${{ matrix.python-version }}
             snakemake
             mamba
-            poetry
+            pandas
           init-shell: bash
           cache-environment: true
           post-cleanup: 'all'
@@ -41,14 +41,8 @@ jobs:
         with:
           singularity-version: 3.7.1
 
-      - name: Install
-        shell: bash -el {0}
-        run: |
-          micromamba activate test-env
-          make install-ci
-
       - name: Test
         shell: bash -el {0}
         run: |
           micromamba activate test-env
-          make test
+          PYTHONPATH="." python -m unittest discover -s tests -t .

pling/__init__.py

@@ -1,14 +0,0 @@
-import sys
-
-"""
-Version has unique source in pyproject.toml.
-importlib fetches version from distribution metadata files
-(in dist-info or egg-info dirs).
-From Python 3.8, importlib_metadata is in standard library as importlib.metadata.
-"""
-if sys.version_info >= (3, 8):
-    from importlib import metadata
-else:
-    import importlib_metadata as metadata
-
-__version__ = metadata.version("pling")

pling/align_snakemake/Snakefile

@@ -40,14 +40,6 @@ rule make_unimogs:
     shadow: "shallow"
     shell:
         """
-        # set conda env first in $PATH - TODO: keep this or manage in other way?
-        # this issue happens when running a pipeline and a conda env is already active but it is not the first
-        # in the $PATH that have python installed (let's call this env E).
-        # In this case, snakemake will activate the "../envs/integerise.yaml" env but the python in the $PATH is the one
-        # in E, which won't have the dependencies required to run the script below.
-        # This is the expected behaviour, is not a bug in conda or snakemake.
-        # For more details, see https://github.com/conda/conda/issues/9392#issuecomment-1291041085
-        PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
         PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/align_snakemake/unimog.py \
             --genomes_list {params.genomes_list} \
             --batch {params.batch} \

pling/anno_snakemake/Snakefile

@@ -115,14 +115,6 @@ rule consolidation:
         outputpath = OUTPUTPATH,
         pling_root_dir = get_pling_root_dir()
     shell: """
-        # set conda env first in $PATH - TODO: keep this or manage in other way?
-        # this issue happens when running a pipeline and a conda env is already active but it is not the first
-        # in the $PATH that have python installed (let's call this env E).
-        # In this case, snakemake will activate the "../envs/integerise.yaml" env but the python in the $PATH is the one
-        # in E, which won't have the dependencies required to run the script below.
-        # This is the expected behaviour, is not a bug in conda or snakemake.
-        # For more details, see https://github.com/conda/conda/issues/9392#issuecomment-1291041085
-        PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
         python {params.pling_root_dir}/pling/anno_snakemake/consolidation.py {params.pafs} "{params.genomes}" {output.unimog} {output.map}
     """
 
@@ -159,14 +151,6 @@ if config.get("dedup", False):
             genomes = lambda wildcards: COMMUNITY_TO_PLASMID[wildcards.community],
             pling_root_dir = get_pling_root_dir()
         shell: """
-            # set conda env first in $PATH - TODO: keep this or manage in other way?
-            # this issue happens when running a pipeline and a conda env is already active but it is not the first
-            # in the $PATH that have python installed (let's call this env E).
-            # In this case, snakemake will activate the "../envs/integerise.yaml" env but the python in the $PATH is the one
-            # in E, which won't have the dependencies required to run the script below.
-            # This is the expected behaviour, is not a bug in conda or snakemake.
-            # For more details, see https://github.com/conda/conda/issues/9392#issuecomment-1291041085
-            PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
             python {params.pling_root_dir}/pling/anno_snakemake/multipartite.py \
                 {input.fasta} {input.unimog} {input.map} \
                 {params.pafs} {params.nucmer_threshold} "{params.genomes}" \
@@ -189,14 +173,6 @@ rule blocks:
         relabelled_dir = f"{OUTPUTPATH}/unimogs/relabelled/blocks",
         pling_root_dir = get_pling_root_dir()
     shell: """
-        # set conda env first in $PATH - TODO: keep this or manage in other way?
-        # this issue happens when running a pipeline and a conda env is already active but it is not the first
-        # in the $PATH that have python installed (let's call this env E).
-        # In this case, snakemake will activate the "../envs/integerise.yaml" env but the python in the $PATH is the one
-        # in E, which won't have the dependencies required to run the script below.
-        # This is the expected behaviour, is not a bug in conda or snakemake.
-        # For more details, see https://github.com/conda/conda/issues/9392#issuecomment-1291041085
-        PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
         python {params.pling_root_dir}/pling/anno_snakemake/blocks.py \
             {input} \
             "{params.genomes}" {params.relabelled_dir} \

pling/batching/Snakefile

@@ -41,7 +41,6 @@ rule get_batches:
     conda: "../envs/smash.yaml"
     shell:
         """
-        PATH="$CONDA_PREFIX"/bin:$PATH
         PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/batching/get_batches.py \
             --genomes_list {params.genomes_list} \
             --batch_size {params.batch_size} \

pling/dcj_snakemake/Snakefile

@@ -47,7 +47,6 @@ if config["ilp_solver"] == "GLPK":
         shadow: "shallow"
         shell:
                 """
-                PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
                 PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/dcj_snakemake/glpk_and_ding.py \
                         --batch {params.batch} \
                         --jaccard_tsv {input.jaccard_tsv} \
@@ -81,7 +80,6 @@ elif config["ilp_solver"] == "gurobi":
         shadow: "shallow"
         shell:
                 """
-                PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
                 PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/dcj_snakemake/gurobi_and_ding.py \
                         --batch {params.batch} \
                         --jaccard_tsv {input.jaccard_tsv} \

pling/jac_network_snakemake/Snakefile

@@ -37,14 +37,6 @@ rule pairwise_seq_jaccard:
         pling_root_dir = get_pling_root_dir()
     shadow: "shallow"
     shell: """
-        # set conda env first in $PATH - TODO: keep this or manage in other way?
-        # this issue happens when running a pipeline and a conda env is already active but it is not the first
-        # in the $PATH that have python installed (let's call this env E).
-        # In this case, snakemake will activate the "../envs/integerise.yaml" env but the python in the $PATH is the one
-        # in E, which won't have the dependencies required to run the script below.
-        # This is the expected behaviour, is not a bug in conda or snakemake.
-        # For more details, see https://github.com/conda/conda/issues/9392#issuecomment-1291041085
-        PATH="$CONDA_PREFIX"/bin:$PATH  # quick fix for the issue described above
         PYTHONPATH={params.pling_root_dir} python {params.pling_root_dir}/pling/jac_network_snakemake/seq_jaccard.py \
             --genomes_list {params.genomes_list} \
             --batch {params.batch} \