fix: Change version and get contrast filename (#1)

* fix: Make frictionless == 4

* refactor: Get filename before contrast_df merge

* style: Run black and isort

* ci: Remove py37

* refactor: Increase min version to 3.8

* Bump version: 0.9.5 → 0.9.6

.github/workflows/test_and_lint.yml

@@ -12,23 +12,22 @@ jobs:
       - uses: actions/setup-python@v2
       - uses: psf/black@stable
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install .
-        pip install pytest
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          pip install pytest
+      - name: Test with pytest
+        run: |
+          pytest

CITATION.cff

@@ -8,5 +8,5 @@ authors:
     given-names: "Rodrigo Juliani"
     orcid: https://orcid.org/0000-0002-1688-6155
 title: "MicroView"
-version: 0.9.5
+version: 0.9.6
 url: "https://github.com/jvfe/microview"

microview/__init__.py

@@ -1,4 +1,4 @@
 name = "microview"
 __author__ = """João Vitor F. Cavalcante"""
 __email__ = "[email protected]"
-__version__ = "0.9.5"
+__version__ = "0.9.6"

microview/file_finder.py

@@ -120,7 +120,6 @@ def detect_report_type(report_paths: List[Path], console) -> List[Sample]:
         console.print("\n Could not find any valid reports", style="red")
         raise Exception("Could not find any valid files.")
     else:
-
         kraken_not_in_kaiju = list(
             filter(lambda report: report not in kaiju_reports, kraken_reports)
         )

microview/parse_taxonomy.py

@@ -46,7 +46,6 @@ def parse_kaiju2table(sample_name: str, df, parsed_stats: Dict) -> None:
     Parses kaiju report
     """
     for row in df.itertuples():
-
         row_dict = {"n_reads": row.reads, "percent": row.percent}
         if row.taxon_name == "unclassified":
             parsed_stats[sample_name].update({"unclassified": row_dict})

microview/plotting.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from typing import Dict, Optional
 
 from plotly import io
@@ -52,7 +53,6 @@ def plot_common_taxas(common_taxas_df, **kwargs):
             "index": "Sample name",
             "value": "% of reads",
             "variable": "Taxon name",
-            "group": "Group",
         },
         template="plotly_white",
         color_discrete_sequence=colors.qualitative.Alphabet,
@@ -70,7 +70,7 @@ def plot_abund_div(abund_div_df, **kwargs):
         y="Shannon Diversity",
         size="N Taxas",
         hover_data=["index"],
-        labels={"group": "Group", "N Taxas": "# taxas"},
+        labels={"N Taxas": "# taxas"},
         template="plotly_white",
         color_discrete_sequence=colors.qualitative.Safe[3:],
         **kwargs,
@@ -86,7 +86,7 @@ def plot_beta_pcoa(beta_pcoa, **kwargs):
         x="PC1",
         y="PC2",
         hover_data=["sample"],
-        labels={"sample": "Sample name", "group": "Group"},
+        labels={"sample": "Sample name"},
         template="plotly_white",
         **kwargs,
     )
@@ -157,6 +157,9 @@ def generate_taxo_plots(tax_data: Dict, contrast_df=None) -> Dict:
 
     # TODO: Improve this check
     if contrast_df is not None and "group" in contrast_df.columns:
+        contrast_df["sample"] = [
+            str(Path(s).name) for s in contrast_df["sample"].to_list()
+        ]
         merged_taxas_df = merge_with_contrasts(tax_data["common taxas"], contrast_df)
 
         common_taxas = plot_common_taxas(merged_taxas_df, facet_col="group")

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.5
+current_version = 0.9.6
 commit = True
 tag = True
 

setup.py

@@ -6,7 +6,7 @@
     readme = readme_file.read()
 
 install_requirements = [
-    "scipy<=1.8",
+    "scipy",
     "scikit-bio",
     "pandas",
     "numpy",
@@ -15,7 +15,7 @@
     "rich",
     "rich-click",
     "click-option-group",
-    "frictionless",
+    "frictionless==4.32.0",
 ]
 
 test_requirements = [
@@ -36,13 +36,13 @@
 setup(
     author="João Vitor F. Cavalcante",
     author_email="[email protected]",
-    python_requires=">=3.7",
+    python_requires=">=3.8",
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
         "Natural Language :: English",
     ],
     description="Generate reports from metagenomics data",
@@ -64,6 +64,6 @@
         "Documentation": "https://jvfe.github.io/microview/",
         "Source Code": "https://github.com/jvfe/microview",
     },
-    version="0.9.5",
+    version="0.9.6",
     zip_safe=False,
 )