fix: make sure code runs with python 3.9

To make the installation easier, drop clapper dependency and test against python 3.9
Also point to stable docs.

.github/workflows/pre-commit.yml

@@ -18,5 +18,5 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.9"
     - uses: pre-commit/[email protected]

.github/workflows/publish-pypi.yml

@@ -23,7 +23,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.9"
 
       - name: Build release distributions
         run: |

README.md

@@ -5,7 +5,7 @@ SPDX-FileContributor: Amir Mohammadi  <[email protected]>
 SPDX-License-Identifier: GPL-3.0-or-later
 -->
 
-[![latest-docs](https://img.shields.io/badge/docs-latest-orange.svg)](https://gridtk.readthedocs.io/en/latest/)
+[![docs](https://img.shields.io/badge/docs-stable-orange.svg)](https://gridtk.readthedocs.io/en/stable/)
 [![build](https://github.com/idiap/gridtk/actions/workflows/build.yml/badge.svg)](https://github.com/idiap/gridtk/actions/workflows/build.yml)
 [![coverage](https://raw.githubusercontent.com/idiap/gridtk/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/idiap/gridtk/blob/python-coverage-comment-action-data/htmlcov/index.html)
 [![repository](https://img.shields.io/badge/github-project-0000c0.svg)](https://github.com/idiap/gridtk)
@@ -26,22 +26,20 @@ installation, submission, monitoring, and various commands provided by GridTK.
 Before diving into GridTK, ensure you have the following prerequisites:
 
 1. A working SLURM setup.
-2. [Pixi](https://pixi.sh) installed.
+2. [pipx](https://pipx.pypa.io/stable/) installed.
 3. GridTK installed (instructions provided below).
 
 ## Installation
 
 To install GridTK, open your terminal and run the following command:
 
 ```bash
-$ pixi global install pipx
-$ pixi global install python=3.12
-$ pipx install --force --python python3.12 'git+https://github.com/idiap/gridtk.git'
+$ pipx install gridtk
 ```
 It is **not recommennded** to install GridTK using `pip install gridtk` in the
 same environment as your expeirments. GirdTK does not need to be installed in
 the same environment as your experiments and its depencencies may conflict with
-your experiments.
+your experiments' dependencies.
 
 ## Basic Usage
 

pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "hatchling.build"
 [project]
 name = "gridtk"
 dynamic = ["version"]
-requires-python = ">=3.12"
+requires-python = ">=3.9"
 description = "GridTK: SLURM Job Managetment for Humans"
 readme = "README.md"
 license = "GPL-3.0-or-later"
@@ -27,12 +27,7 @@ classifiers = [
   "Programming Language :: Python :: 3",
   "Topic :: System :: Distributed Computing",
 ]
-dependencies = [
-  "clapper~=1.1",
-  "sqlalchemy~=2.0",
-  "tabulate~=0.9.0",
-  "click~=8.1",
-]
+dependencies = ["sqlalchemy~=2.0", "tabulate~=0.9.0", "click~=8.1"]
 
 [project.urls]
 documentation = "https://gridtk.readthedocs.io/en/latest/"
@@ -76,6 +71,9 @@ self = { solve-group = "default" }
 test = { features = ["test"], solve-group = "default" }
 doc = { features = ["doc"], solve-group = "default" }
 
+[tool.pixi.dependencies]
+python = "3.9.*"
+
 [tool.hatch.version]
 source = "versioningit"
 
@@ -104,7 +102,7 @@ packages = ["src/gridtk"]
 
 [tool.ruff]
 line-length = 88
-target-version = "py312"
+target-version = "py39"
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -170,4 +168,4 @@ junit_log_passing_tests = false
 relative_files = true
 
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.9"

src/gridtk/cli.py

@@ -8,27 +8,37 @@
 
 from collections import defaultdict
 from pathlib import Path
+from typing import Optional
 
 import click
 
-from clapper.click import AliasedGroup
 
-
-class CustomGroup(AliasedGroup):
+class CustomGroup(click.Group):
     """Custom command group that does not sort commands."""
 
     def list_commands(self, ctx: click.Context) -> list[str]:
         # do not sort the commands
         return self.commands
 
     def get_command(self, ctx, cmd_name):
+        """get_command with prefix aliasing and name aliases."""
         cmd_name = {
             "sbatch": "submit",
             "ls": "list",
             "rm": "delete",
             "remove": "delete",
         }.get(cmd_name, cmd_name)
-        return super().get_command(ctx, cmd_name)
+        rv = click.Group.get_command(self, ctx, cmd_name)
+        if rv is not None:
+            return rv
+        matches = [x for x in self.list_commands(ctx) if x.startswith(cmd_name)]
+        if not matches:
+            return None
+
+        if len(matches) == 1:
+            return click.Group.get_command(self, ctx, matches[0])
+
+        ctx.fail(f"Too many matches: {', '.join(sorted(matches))}")  # noqa: RET503
 
 
 @click.group(
@@ -453,7 +463,7 @@ def report(
     states: list[str],
     names: list[str],
     dependents: bool,
-    array_idx: str | None,
+    array_idx: Optional[str],
 ):
     """Report on jobs in the queue."""
     from .manager import JobManager

src/gridtk/manager.py

@@ -2,6 +2,7 @@
 # SPDX-FileContributor: Amir Mohammadi  <[email protected]>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+
 """Implements a Slurm job manager. Jobs are kept track of in an SQL database
 and logs are written to a default logs folder.
 

src/gridtk/models.py

@@ -2,6 +2,7 @@
 # SPDX-FileContributor: Amir Mohammadi  <[email protected]>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+
 import json
 import re
 import shlex
@@ -11,6 +12,7 @@
 
 from pathlib import Path
 from sqlite3 import Connection as SQLite3Connection
+from typing import Optional
 
 from sqlalchemy import Column, ForeignKey, Integer, String, Table, event
 from sqlalchemy.engine import Engine
@@ -80,7 +82,7 @@ class ObjectValue(TypeDecorator):
 
     def process_bind_param(self, value, dialect):
         if value is not None:
-            if isinstance(value, dict | list | tuple):
+            if isinstance(value, (dict, list, tuple)):
                 value = json.dumps(value)
             elif isinstance(value, Path):
                 value = str(value.absolute())
@@ -141,12 +143,12 @@ class Job(Base):
     command: Mapped[list] = mapped_column(ObjectValue)
     logs_dir: Mapped[Path] = mapped_column(ObjectValue)
     is_array_job: Mapped[bool]
-    dependencies_str: Mapped[str | None] = mapped_column(String(2048))
-    grid_id: Mapped[int | None]
-    state: Mapped[str | None] = mapped_column(String(30), default="UNKNOWN")
-    exit_code: Mapped[str | None]
-    nodes: Mapped[str | None]  # list of node names
-    array_task_ids: Mapped[list[int] | None] = mapped_column(ObjectValue)
+    dependencies_str: Mapped[Optional[str]] = mapped_column(String(2048))
+    grid_id: Mapped[Optional[int]]
+    state: Mapped[Optional[str]] = mapped_column(String(30), default="UNKNOWN")
+    exit_code: Mapped[Optional[str]]
+    nodes: Mapped[Optional[str]]  # list of node names
+    array_task_ids: Mapped[Optional[list[int]]] = mapped_column(ObjectValue)
     dependencies_jobdependency: Mapped[list[JobDependency]] = relationship(
         JobDependency,
         primaryjoin=id == JobDependency.job_id,  # type: ignore[attr-defined]
@@ -237,14 +239,17 @@ def submitted_command(self, fh, session):
         ] + command
 
     def submit(self, session: Session = None):
-        with tempfile.NamedTemporaryFile(
-            mode="w+t", suffix=".sh", delete_on_close=False
-        ) as fh:
-            command = self.submitted_command(fh=fh, session=session)
-            output = subprocess.check_output(
-                command,
-                text=True,
-            )
+        with tempfile.NamedTemporaryFile(mode="w+t", suffix=".sh", delete=False) as fh:
+            try:
+                command = self.submitted_command(fh=fh, session=session)
+                output = subprocess.check_output(
+                    command,
+                    text=True,
+                )
+            finally:
+                # remove the temporary file here because we don't want it
+                # deleted after fh.close() is called
+                Path(fh.name).unlink(missing_ok=True)
         # find job ID from output
         # output is like b'Submitted batch job 123456789\n'
         self.grid_id = int(re.search("[0-9]+", output).group())

src/gridtk/tools.py

@@ -2,8 +2,11 @@
 # SPDX-FileContributor: Amir Mohammadi  <[email protected]>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
+
 import re
 
+from typing import Optional
+
 
 def parse_array_indexes(indexes_str: str) -> list[int]:
     """Pares a string of array indexes to a list of integers."""
@@ -36,7 +39,7 @@ def parse_segment(segment):
     return result
 
 
-def job_ids_from_dep_str(dependency_string: str | None) -> list[int]:
+def job_ids_from_dep_str(dependency_string: Optional[str]) -> list[int]:
     """Extract job IDs from a dependency string."""
     if not dependency_string:
         return []