Improved tests and removed snakemake pipelines (#30)

* start making the new wipertools repo

* moving devcontainer files together in the sample directory

* settling devcontainer ffiles

* improve functionalities and fix versions

* handling compressed fastq in scatter

* improved implementation of gather and scatter

* improved summary gather implementation

* expanded pytests

* fixing github actions

* fixed pytest action

* fixing pytests

* fixing pytest

* improved code coverage

.coveragerc

@@ -3,4 +3,4 @@ omit = __init__.py
 
 [report]
 exclude_also =
-    def wipe_fastq
+    if __name__ == .__main__.:

.devcontainer/Dockerfile

@@ -0,0 +1,10 @@
+FROM condaforge/mambaforge
+LABEL maintainer="[email protected]"
+
+COPY data data
+COPY ./.devcontainer/environment.yml environment.yml
+
+RUN mamba env update --file environment.yml --name base
+RUN git config --global core.autocrlf true
+
+WORKDIR /fastqwiper

.devcontainer/devcontainer.json

@@ -1,22 +1,24 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
 {
-	"name": "Existing Dockerfile",
-	"build": {
-		// Sets the run context to one level up instead of the .devcontainer folder.
-		"context": "..",
-		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-		"dockerfile": "../Dockerfile"
-	},
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	"features": {
-       "ghcr.io/devcontainers/features/git:1": {}
-    },
-	"customizations" : {
-		"jetbrains" : {
-		  "backend" : "PyCharm"
-		}
-	},
-    workspaceFolder: "/fastqwiper",
-    workspaceMount: "source=${localWorkspaceFolder},target=/fastqwiper,type=bind"
-}
+  "name": "Dockerfile FastqWiper@BFX",
+  "build": {
+    "context": "..",
+    "dockerfile": "Dockerfile"
+  },
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {}
+  },
+  "workspaceFolder": "/fastqwiper",
+  "workspaceMount": "source=${localWorkspaceFolder},target=/fastqwiper,type=bind",
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-python.debugpy",
+        "ms-azuretools.vscode-docker"
+      ]
+    }
+  }
+}

.devcontainer/environment.yml

@@ -0,0 +1,11 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python
+  - pytest
+  - pytest-cov
+  - conda-build
+  - bioconda-utils
+  - pyyaml

.dockerignore

@@ -1,7 +1,6 @@
 .snakemake
 .vscode
 .gitignore
-.devcontainer
 .github
 .pytest_cache
 .coveragerc
@@ -10,6 +9,4 @@ __pycache__
 
 environment.yml
 requirements.txt
-setup.py
 conda-recipe/
-logs/

.github/workflows/code_coverage.yml

@@ -6,40 +6,39 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
-        matrix:
-          os: [ubuntu-latest]  # , macos-latest, windows-latest
+      matrix:
+        os: [ubuntu-latest] # , macos-latest, windows-latest
 
     env:
-        OS: ${{ matrix.os }}
-        PYTHON: '3.11'
+      OS: ${{ matrix.os }}
+      PYTHON: "3.10"
 
     name: Test FastqWiper
     steps:
-    - uses: actions/checkout@v4
-      name: Clone repository
-    
-    - name: Install Miniconda (Mambaforge)
-      uses: conda-incubator/setup-miniconda@v3
-      with:
+      - uses: actions/checkout@v4
+        name: Clone repository
+
+      - name: Install Miniconda (Mambaforge)
+        uses: conda-incubator/setup-miniconda@v3
+        with:
           auto-update-conda: true
           auto-activate-base: true
           show-channel-urls: true
-          channels: conda-forge,defaults
+          channels: conda-forge,bioconda,defaults
           python-version: ${{ env.PYTHON }}
-          environment-file: environment.yml
-          miniforge-variant: Mambaforge
-
-    - name: Run tests and collect coverage
-      shell: bash -el {0}
-      run: pytest --pyargs ./tests --cov-config=.coveragerc --cov=./fastqwiper --cov-report=xml
+          environment-file: .devcontainer/environment.yml
+
+      - name: Run tests and collect coverage
+        shell: bash -el {0}
+        run: pytest --pyargs ./tests --cov-config=.coveragerc --cov=./fastqwiper --cov-report=xml
 
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        env_vars: OS,PYTHON
-        files: ./coverage.xml # optional
-        flags: pytest # optional
-        name: codecov-umbrella # optional
-        fail_ci_if_error: true # optional (default = false)
-        verbose: true # optional (default = false)
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          env_vars: OS,PYTHON
+          files: ./coverage.xml # optional
+          flags: pytest # optional
+          name: codecov-umbrella # optional
+          fail_ci_if_error: true # optional (default = false)
+          verbose: true # optional (default = false)

.gitignore

@@ -1,7 +1,7 @@
 #my custom
-bbmap/
-logs/
-bbmap
+data/*
+!data/sample_R1.fastq.gz
+!data/sample_R2.fastq.gz
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -63,19 +63,6 @@ coverage.xml
 *.mo
 *.pot
 
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
 # Sphinx documentation
 docs/_build/
 

.vscode/launch.json

@@ -0,0 +1,85 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Debugger: summarygather",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolderBasename}/wipertools.py",
+            "console": "integratedTerminal",
+            "args": [
+                "summarygather",
+                "--summaries",
+                "data/abba_full_wiped.fastq.log",
+                "data/abba_full_wiped.fastq2.log",
+                "--final_summary",
+                "data/abba_full_wiped.fastq.summary",
+            ]
+        },
+        {
+            "name": "Debugger: fastqwiper",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolderBasename}/wipertools.py",
+            "console": "integratedTerminal",
+            "args": [
+                "fastqwiper",
+                "--fastq_in",
+                "data/abba_full.fastq",
+                "--fastq_out",
+                "data/abba_full_wiped.fastq",
+                "-f",
+                "10",
+                "-l",
+                "data/abba_full_wiped.fastq.log",
+                "-a",
+                "TCGAN"
+            ]
+        },
+        {
+            "name": "Debugger: fastqscatter",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolderBasename}/wipertools.py",
+            "console": "integratedTerminal",
+            "args": [
+                "fastqscatter",
+                "--fastq",
+                "data/sample_R1.fastq.gz",
+                "--num_splits",
+                "3",
+                "--out_folder",
+                "./data/splits_unix",
+                "--prefix",
+                "ff",
+                "--suffix",
+                "rr",
+                "--ext",
+                "fastq",
+                "--os",
+                "unix"
+            ]
+        },
+        {
+            "name": "Debugger: fastqgather",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${workspaceFolderBasename}/wipertools.py",
+            "console": "integratedTerminal",
+            "args": [
+                "fastqgather",
+                "--in_folder",
+                "data/splits_unix",
+                "--out_fastq",
+                "data/gathered_unix.fastq",
+                "--prefix",
+                "ff",
+                "--os",
+                "unix"
+            ]
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python.analysis.autoImportCompletions": true,
+    "python.analysis.typeCheckingMode": "basic"
+}