rebase with harpy view

.github/filters.yml

@@ -164,7 +164,8 @@ assembly: &assembly
   - 'harpy/snakefiles/assembly.smk'
   - 'harpy/snakefiles/metassembly.smk'
 other: &other
-  - 'harpy/stitchparams.py'
+  - *common
+  - 'harpy/imputeparams.py'
   - 'harpy/popgroup.py'
   - 'harpy/hpc.py'
 modules:

.github/workflows/tests.yml

@@ -822,9 +822,9 @@ jobs:
           resources/buildforCI.sh
       - name: Clear Space
         uses: jlumbroso/free-disk-space@main
-      - name: harpy stitchparams
+      - name: harpy imputeparams
         shell: micromamba-shell {0}
-        run: harpy stitchparams -o params.file
+        run: harpy imputeparams -o params.file
       - name: harpy popgroup
         shell: micromamba-shell {0}
         run: harpy popgroup test/fastq

harpy/__main__.py

@@ -16,8 +16,9 @@
 from . import simulate
 from . import snp
 from . import sv
-from .popgroups import popgroup
+from .popgroup import popgroup
 from .imputeparams import imputeparams
+from . import view
 
 click.rich_click.USE_MARKDOWN = True
 click.rich_click.SHOW_ARGUMENTS = False
@@ -44,6 +45,7 @@ def cli():
 # main program
 cli.add_command(popgroup)
 cli.add_command(imputeparams)
+cli.add_command(view.view)
 cli.add_command(preflight.preflight)
 cli.add_command(demultiplex.demultiplex)
 cli.add_command(qc.qc)
@@ -70,7 +72,7 @@ def cli():
             },
             {
                 "name": "Other Commands",
-                "commands": sorted(["deconvolve", "hpc", "imputeparams", "popgroup","preflight","resume"])
+                "commands": sorted(["deconvolve", "hpc", "imputeparams", "popgroup","preflight","resume", "view"])
             }
         ],
  } | simulate.commandstring | hpc.docstring

harpy/view.py

@@ -0,0 +1,72 @@
+"""View the latest log or snakefile of a workflow"""
+
+import os
+import sys
+import glob
+import subprocess
+import rich_click as click
+from ._printing import print_error
+from ._validations import is_gzip
+
+@click.command(no_args_is_help = True, context_settings=dict(allow_interspersed_args=False))
+@click.option('-s', '--snakefile',  is_flag = True, show_default = True, default = False, help = "View the snakefile, not the log file")
+@click.argument('directory', required=True, type=click.Path(exists=True, file_okay=False))
+def view(directory, snakefile):
+    """
+    View a workflow log file or snakefile
+
+    This convenience command lets you view the latest workflow log file
+    of a Harpy output directory. You can use `--snakefile` to view the workflow
+    snakefile instead. Output is printed to the screen via `less` and
+    accepts the typical keyboard shortcuts to navigate the output, e.g.:
+
+    | key                     | function                   |
+    | :---------------------- | :------------------------- |
+    | `up arrow`/`down arrow` | scroll up/down             |
+    | `Page Up`/`Page Down`   | scroll up/down, but faster |
+    | `q`                     | exit                       |
+    """
+    # check if there is a workflow or log folder
+    # and whether the expected files are in there
+    err = 0
+    if snakefile:
+        files = [i for i in glob.iglob(f"{directory}/workflow/*.smk")]
+        err_dir = f"{directory}/workflow/"
+        err_file = "snakefiles"
+        if not os.path.exists(f"{directory}/workflow"):
+            err = 1
+        elif not files:
+            err = 2
+    else:
+        files = [i for i in glob.iglob(f"{directory}/logs/snakemake/*.log*")]
+        err_dir = f"{directory}/logs/snakemake/"
+        err_file = "log files"
+        if not os.path.exists(f"{directory}/logs/snakemake"):
+            err = 1
+        elif not files:
+            err = 2
+    if err == 1:
+        print_error(
+            "Directory not found", 
+            f"The file you are trying to view is expected to be in [blue]{err_dir}[/blue], but that directory was not found. Please check that this is the correct folder."
+        )
+        sys.exit(1)
+    elif err == 2:
+        print_error(
+            "File not found", 
+            f"There are no {err_file} in [blue]{err_dir}[/blue]. Please check that this is the correct folder."
+        )
+        sys.exit(1)
+    # sort and pull only the most recent file (based on modification time)
+    file = sorted(files, key = os.path.getmtime)[-1]
+    if not os.access(file, os.R_OK):
+        print_error(
+            "Incorrect permissions",
+            f"[blue]{file}[/blue] does not have read access. Please check the file permissions."
+        )
+        sys.exit(1)
+
+    cat_cmd = "zcat" if is_gzip(file) else "cat"
+    stream = subprocess.Popen([cat_cmd, file], stdout=subprocess.PIPE)
+    pygment = subprocess.Popen(["pygmentize", "-l", "yaml"], stdin = stream.stdout, stdout = subprocess.PIPE)
+    subprocess.run(["less", "-R"], stdin = pygment.stdout) 

pyproject.toml

@@ -14,15 +14,14 @@ readme = {file = "README.md", content-type = "text/markdown"}
 license = {text = "GPL-3.0"}
 
 [tool.setuptools.packages.find]
-where = ["."]
+include = ["harpy"]
+exclude = ["test"]
 
 [tool.setuptools.package-data]
 "*" = ["*.*"]
 
 [project.scripts]
 harpy = "harpy.__main__:cli"
 
-[tool.setuptools_scm]
-
 [project.urls]
 Homepage = "https://github.com/pdimens/harpy"

resources/buildlocal.sh

@@ -12,8 +12,8 @@ mkdir -p ${CONDA_PREFIX}/bin
 g++ harpy/bin/extractReads.cpp -O3 -o ${CONDA_PREFIX}/bin/extractReads
 
 # install harpy proper
-pip install . --no-deps && \
-    rm -r build harpy.egg-info
+pip install --no-deps --disable-pip-version-check -e . && \
+    rm -rf build #harpy.egg-info
 
 # associated scripts
 chmod +x harpy/bin/*