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formast/commitdif.py

+import csv
+import git
+import click
+#import getfile as gf
+from tqdm import tqdm
+
+@click.command()
+@click.argument("repo")
+@click.argument("output")    
+def main(repo, output):
+    # Open the output CSV file for writing
+    with open(output, "w") as f:
+        repo = git.Repo(repo)
+        writer = csv.writer(f)
+
+        # Write the header row
+        writer.writerow(["commit_hash", "num_additions", "num_deletions", "filename"])
+
+        # Loop through the commits and get the diff stats
+        for commit in tqdm(list(repo.iter_commits())):
+            if len(parrent := commit.parents) != 1:
+                continue
+
+            diff = repo.git.diff(parrent, commit, numstat=True)
+            for line in diff.splitlines():
+                num_additions, num_deletions, filename = line.split("\t")
+                writer.writerow([commit.hexsha, num_additions, num_deletions, filename])
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file

formast/formastrepo.py

+from contextlib import contextmanager
+from pathlib import Path
+import shutil
+from typing import Callable
+import click
+import csv
+import git
+import os
+import git_filter_repo as fr
+import tempfile
+import subprocess
+import logging
+from dataclasses import dataclass, field
+
+log = logging.getLogger("regit")
+
+# Some code borrowed from https://github.com/newren/git-filter-repo/blob/main/contrib/filter-repo-demos/lint-history
+
+
+class Executable(click.ParamType):
+    name = "executable"
+
+    def convert(self, value, param, ctx):
+        if "/" in value:
+            exe = Path(value)
+            exe = exe.absolute()
+            if not os.access(exe, os.X_OK):
+                self.fail(f"{value!r} is not an executable file", param, ctx)
+        else:
+            pp = shutil.which(value)
+            if pp is None:
+                self.fail(
+                    f"Could not find {value!r} on path, add './' if it is a file.",
+                    param,
+                    ctx,
+                )
+            exe = Path(pp)
+        return exe
+
+
+@contextmanager
+def blob_reader():
+    process = subprocess.Popen(
+        ["git", "cat-file", "--batch"], stdin=subprocess.PIPE, stdout=subprocess.PIPE
+    )
+
+    def reader(blob_id):
+        assert process.stdin is not None
+        assert process.stdout is not None
+        process.stdin.write(blob_id + b"\n")
+        process.stdin.flush()
+        _, _, objsize = process.stdout.readline().split()
+        return process.stdout.read(int(objsize) + 1)[:-1]
+
+    yield reader
+
+    if process.stdin is not None:
+        process.stdin.close()
+
+    process.wait()
+
+
+@dataclass
+class BlobHandler:
+    reader: Callable[[str], bytes]
+    filter: fr.RepoFilter | None = None
+    blobs_handled: dict[int, int] = field(default_factory=dict)
+    is_relevant: Callable[[Path], bool] = lambda _: True
+    transform: Callable[[Path, bytes], bytes] = lambda _, b: b
+
+    def __call__(self, commit: fr.Commit, metadata):
+        assert self.filter is not None
+        for change in commit.file_changes:
+            filename = Path(change.filename.decode("utf-8"))
+            if change.type == b"D" or not self.is_relevant(filename):
+                continue
+
+            if change.blob_id not in self.blobs_handled:
+                content = self.reader(change.blob_id)
+                blob = fr.Blob(self.transform(filename, content))
+                self.filter.insert(blob)
+                # Record our handling of the blob and use it for this change
+                self.blobs_handled[change.blob_id] = blob.id
+            change.blob_id = self.blobs_handled[change.blob_id]
+
+
+@contextmanager
+def tfile(folder, filename, content):
+    tmp_file = folder / filename
+    with open(tmp_file, "wb") as f:
+        f.write(content)
+    yield tmp_file
+    os.remove(tmp_file)
+
+
+def transform_program(program: Path, args: tuple[str], folder: Path):
+    def callback(file: Path, content: bytes):
+        pargs = list(args)
+        try:
+            ix = pargs.index("{}")
+        except ValueError:
+            cmd = [program] + pargs
+            log.debug("Running cmd %s", cmd)
+            return subprocess.run(
+                cmd, input=content, capture_output=True, check=True
+            ).stdout
+        else:
+            with tfile(folder, file.name, content) as tmp_file:
+                pargs[ix] = str(tmp_file)
+                cmd = [program] + pargs
+                log.debug("Running cmd %s", cmd)
+                subprocess.run(cmd, check=True)
+                with open(tmp_file, "rb") as f:
+                    return f.read()
+
+    return callback
+
+
+@click.command()
+@click.option("--repo", help="the repo to clone and change", default=None)
+@click.option(
+    "-o",
+    "--output",
+    help="The name of the resulting repo",
+    type=click.Path(exists=False, path_type=Path),
+)
+@click.option(
+    "-p",
+    "--pattern",
+    help="the glob-pattern to match files.",
+    type=str,
+)
+@click.option(
+    "-m",
+    "--mapping",
+    help="The file to output the csv mapping to",
+    type=click.File("w", lazy=False),
+)
+@click.option(
+    "-v",
+    "--verbose",
+    help="The verbosity of logging",
+    count=True,
+)
+@click.argument(
+    "program",
+    # help="The program to execute on each file",
+    type=Executable(),
+)
+@click.argument(
+    "args",
+    # help="The argurments, choose '{}' to mean the file in question, omit a '{}' to use stdin",
+    nargs=-1,
+    type=str,
+)
+def regit(
+    repo,
+    pattern: str | None,
+    output: Path,
+    mapping,
+    program: Path,
+    args: tuple[str],
+    verbose: int,
+):
+    """A simple program that runs a command on every commit on a repo."""
+
+    logging.basicConfig(level=verbose)
+    log.debug("Setting verbosity %s", verbose)
+
+    if output is None:
+        output = Path(tempfile.mkdtemp())
+
+    if repo is None:
+        repo = git.Repo().clone(path=output)
+    else:
+        repo = git.Repo.clone_from(url=repo, to_path=output)
+
+    os.chdir(output)
+    options = fr.FilteringOptions.parse_args([], error_on_empty=False)
+
+    with blob_reader() as br, tempfile.TemporaryDirectory() as folder:
+        handler = BlobHandler(
+            br,
+            is_relevant=lambda a: pattern is None or a.match(pattern),
+            transform=transform_program(program, args, Path(folder)),
+        )
+        filter = fr.RepoFilter(options, commit_callback=handler)
+        handler.filter = filter
+        filter.run()
+
+        if mapping:
+            writer = csv.writer(mapping)
+            writer.writerow(["from", "to"])
+            for fm, to in filter._commit_renames.items():
+
+                def handle(a):
+                    if isinstance(a, bytes):
+                        return a.decode()
+                    else:
+                        log.warning("Unexpected result %s", a)
+                        return str(a)
+
+                writer.writerow([handle(m) for m in [fm, to]])
+
+    print(output)
+
+
+if __name__ == "__main__":
+    regit()

formast/getfile.py

+import click
+import os
+from git import Repo
+
+
+@click.command()
+def main():
+    
+    repo = get_repo()
+
+    # Get all Java files in the repository
+    java_files = []
+    for root, dirs, files in os.walk(repo.working_tree_dir):
+        for file in files:
+            if file.endswith(".java"):
+                java_files.append(file)
+    
+    # List the Java files from the repository if there are any
+    # if java_files:
+    #     click.echo("The Java files in the repository are:")
+    #     for file in java_files:
+    #         click.echo(file)
+    #     click.echo("Total number of Java files: " + str(len(java_files)))
+    # else:
+    #     click.echo("No Java files found in the repository.")
+    click.echo("Total number of Java files: " + str(len(java_files)))
+
+
+    # Get commit history of the repository
+    for commit in repo.iter_commits():
+        print(f"commit: {commit.hexsha}")
+        print(f"author: {commit.author}")
+        print(f"date: {commit.committed_datetime}")
+        print(f"message: {commit.message}")
+        print()
+
+    return java_files
+
+def get_repo():
+    choice = click.prompt("Clone a new repository or choose a local repository", type=click.Choice(['clone', 'local'], case_sensitive=False))
+    
+    # User chooses to clone a new repository
+    if choice == 'clone':
+        url = click.prompt("Enter URL for GitHub repository")
+        default_path = os.path.expanduser("~") + "/repos"
+        path = click.prompt("Enter path to clone the repository or press enter to use the default path", default=default_path, type=click.Path(exists=True, file_okay=False, dir_okay=True, writable=True))
+        repo = Repo.clone_from(url, path)
+        click.echo(f"Repository cloned to {repo.working_tree_dir}")
+
+    # User chooses to use a local repository  
+    elif choice == 'local':
+        path = click.prompt("Enter path to local repository", type=click.Path(exists=True, file_okay=False, dir_okay=True))
+        repo = Repo(path)
+        click.echo(f"Repository at {repo.working_tree_dir}")
+
+        return repo
+    
+# Get all the java files in the repository
+def get_java_files(repo):
+    java_files = []
+    for root, dirs, files in os.walk(repo.working_tree_dir):
+        for file in files:
+            if file.endswith(".java"):
+                java_files.append(file)
+    
+    return java_files
+
+
+    
+if __name__ == '__main__':
+    main()

pyproject.toml

@@ -8,6 +8,13 @@ authors = [
 dependencies = [
     "click>=8.1.3",
     "tree-sitter>=0.20.1",
+    "GitPython>=3.1.31",
+    "tqdm>=4.65.0",
+    "git-filter-repo>=2.38.0",
+    "jupyter>=1.0.0",
+    "pandas>=1.5.3",
+    "regit @ file:///${PROJECT_ROOT}/../../regit",
+    "matplotlib>=3.7.1",
 ]
 requires-python = ">=3.10"
 readme = "README.md"
@@ -21,4 +28,8 @@ requires = ["pdm-pep517>=1.0"]
 build-backend = "pdm.pep517.api"
 
 [tool.pdm]
-
+[tool.pdm.build]
+excludes = ["./**/.git"]
+package-dir = "src"
+includes = ["src/formast"]
+source-includes = ["LICENSE", "README.md"]
\ No newline at end of file

formast/__main__.py → src/formast/__main__.py

@@ -2,32 +2,58 @@ import click
 import os
 from tree_sitter import Language, Parser
 
-Language.build_library(
-    # Store the library in the `build` directory
-    'build/my-languages.so',
+import logging
 
-    # Include one or more languages
-    [
-        '../../vendor/tree-sitter-java'
-    ]
-)
-JAVA_LANGUAGE = Language('build/my-languages.so', 'java')
+from pathlib import Path
 
-parser = Parser()
-parser.set_language(JAVA_LANGUAGE)
+log = logging.getLogger(__name__)
 
+# Language.build_library(
+#     # Store the library in the `build` directory
+#     'build/my-languages.so',
 
-@click.command()
-@click.option("--file", prompt="Path of the file", help="Path of the file")    
-def cli(file):
-    formast(file)
-#@click.option("--file2", prompt="Path of the second file", help="Path of the second file")
+#     # Include one or more languages
+#     [
+#         '../../vendor/tree-sitter-java'
+#     ]
+# )
 
+
+@click.command()
+@click.option("--overwrite", is_flag=True, help="Overwrite the original .java file with the .ast content")
+@click.option("-v", "--verbose", count=True, help="Increase output verbosity")
+@click.argument("file_path", type=click.Path(exists=True))
 ## Formast 
-def formast(file_path):
-    tree = parse_java_file(file_path)  
+def formast(file_path, overwrite, verbose):
+
+    # initialize logging
+    logging.basicConfig(level=verbose)
+
+    log.info("Formast v0.1.0")
+
+    # Load the language (assuming the language is created, if not run the commented code above)
+    language_file = Path(__file__).absolute().parent.parent.parent / 'build' / 'my-languages.so'
+    log.debug("Using language file: %s", language_file)
+    JAVA_LANGUAGE = Language(str(language_file), 'java')
+    parser = Parser()
+    parser.set_language(JAVA_LANGUAGE)
+    log.info("Sucessfully created parser.")
+
+    log.info(f"Processing {file_path}...")
+    tree = parse_java_file(parser, file_path)  
     save_ast_file(file_path, tree)
-    print("AST file saved!")
+
+    # If overwrite is true, overwrite the original .java file with the .ast content
+    if overwrite:
+        with open(file_path+".ast", 'r') as ast_file:
+            ast_content = ast_file.read()
+        with open(file_path, 'w') as java_file:
+            java_file.write(ast_content)
+        os.remove(file_path+".ast")
+        log.info("Original .java file overwritten with .ast content!")
+    else:
+        log.info("AST file saved!")
+
 
 ## Tree traversal function
 def traverse(tree):
@@ -48,7 +74,7 @@ def traverse(tree):
             break
 
 ## Parse the java file and return the tree
-def parse_java_file(file_path):
+def parse_java_file(parser, file_path):
     if not is_java_file(file_path):
         raise ValueError('File must have a .java extension')
     
@@ -67,12 +93,9 @@ def save_ast_file(file_path, tree):
                 f.write(node.text.decode("utf8"))
                 f.write("\n")
 
-
 ## Check if the file is a java file
 def is_java_file(file_path):
     return os.path.splitext(file_path)[1] == '.java'
 
-
-
 if __name__ == "__main__":
-    cli()
+    formast()
\ No newline at end of file