Repository: yandex/ch-tools
Pull request #330: Update dependencies and drop usage of deprecated docker compose v1
Author: login: Alex-Burmak
Created: 2025-05-22T09:04:32Z | Merged: 2025-05-23T09:25:39Z

## Summary by Sourcery

Modernize dependencies, bump Python requirement, and enforce environment prerequisites including Docker Compose v2 in the Makefile and project configuration.

New Features:
- Add Makefile targets to validate presence of uv, Docker, and Docker Compose
- Introduce CLICKHOUSE_VERSION environment variable with default 'latest'

Enhancements:
- Raise Python requirement to >=3.9 and update version constraints for key dependencies and dev tools
- Replace deprecated docker-compose v1 usage by requiring Docker Compose v2 syntax in build and test targets
- Simplify and inline DeepDiff configuration and cleanup minor code formatting inconsistencies


Diff:
diff --git a/Makefile b/Makefile
index 920985c3..256e5cb2 100644
--- a/Makefile
+++ b/Makefile
@@ -24,6 +24,8 @@ else
 	export PYTHON_VERSION := $(shell cat .python-version)
 endif
 
+export CLICKHOUSE_VERSION ?= latest
+
 PREFIX ?= /opt/yandex/$(PROJECT_NAME)
 export BUILD_PYTHON_OUTPUT_DIR ?= dist
 export BUILD_DEB_OUTPUT_DIR ?= out
@@ -70,7 +72,7 @@ build: setup build-python-packages
 
 
 .PHONY: setup
-setup: check-environment $(VERSION_FILE)
+setup: check-uv $(VERSION_FILE)
 
 
 .PHONY: all
@@ -127,7 +129,7 @@ test-unit: setup
 
 
 .PHONY: test-integration
-test-integration: build-python-packages
+test-integration: check-docker-compose build-python-packages
 	cd $(TESTS_DIR)
 	export PYTHONPATH=$(CURDIR):$$PATH
 	uv run behave --show-timings --stop --junit $(BEHAVE_ARGS)
@@ -244,13 +246,6 @@ prepare-changelog: setup
 	DEBFULLNAME="Yandex LLC" DEBEMAIL="ch-tools@yandex-team.ru" dch --force-bad-version --distribution stable -v $$(cat $(VERSION_FILE)) Autobuild
 
 
-.PHONY: check-environment
-check-environment:
-	@if ! command -v "uv" &>/dev/null; then \
-		echo 'Python project manager tool "uv" not found. Please follow installation instructions at https://docs.astral.sh/uv/getting-started/installation.' >&2; exit 1; \
-	fi
-
-
 $(VERSION_FILE):
 	echo "2.$$(git rev-list HEAD --count).$$(git rev-parse --short HEAD | xargs -I {} printf '%d' 0x{})" > $@
 
@@ -261,7 +256,7 @@ prepare-build-deb:
 
 
 .PHONY: build-deb-package
-build-deb-package: setup
+build-deb-package: check-docker setup
 	./build_deb_in_docker.sh
 
 
@@ -286,6 +281,27 @@ clean: clean_debuild
 	rm -rf .mypy_cache .ruff_cache tests/{.session_conf.sav,__pycache__,staging,reports}
 
 
+.PHONY: check-uv
+check-uv:
+	@if ! command -v "uv" &>/dev/null; then \
+		echo 'Python project manager tool "uv" not found. Please follow installation instructions at https://docs.astral.sh/uv/getting-started/installation.' >&2; exit 1; \
+	fi
+
+
+.PHONY: check-docker
+check-docker:
+	@if ! command -v "docker" &>/dev/null; then \
+		echo 'Docker not found. Please follow installation instructions at https://docs.docker.com/engine/install.' >&2; exit 1; \
+	fi
+
+
+.PHONY: check-docker-compose
+check-docker-compose: check-docker
+	@if ! (docker compose version || docker-compose version) &>/dev/null; then \
+		echo 'Docker Compose not found. Please follow installation instructions at https://docs.docker.com/compose/install.' >&2; exit 1; \
+	fi
+
+
 .PHONY: help
 help:
 	echo "Targets:"
diff --git a/ch_tools/chadmin/cli/object_storage_group.py b/ch_tools/chadmin/cli/object_storage_group.py
index f381c473..225bde75 100644
--- a/ch_tools/chadmin/cli/object_storage_group.py
+++ b/ch_tools/chadmin/cli/object_storage_group.py
@@ -42,10 +42,10 @@
 def object_storage_group(ctx: Context, disk_name: str) -> None:
     """Commands to manage S3 objects and their metadata."""
     ch_config = get_clickhouse_config(ctx)
-    ctx.obj[
-        "disk_configuration"
-    ] = ch_config.storage_configuration.s3_disk_configuration(
-        disk_name, ctx.obj["config"]["object_storage"]["bucket_name_prefix"]
+    ctx.obj["disk_configuration"] = (
+        ch_config.storage_configuration.s3_disk_configuration(
+            disk_name, ctx.obj["config"]["object_storage"]["bucket_name_prefix"]
+        )
     )
 
 
diff --git a/ch_tools/chadmin/internal/object_storage/s3_iterator.py b/ch_tools/chadmin/internal/object_storage/s3_iterator.py
index 252c7dfc..15e5262e 100644
--- a/ch_tools/chadmin/internal/object_storage/s3_iterator.py
+++ b/ch_tools/chadmin/internal/object_storage/s3_iterator.py
@@ -13,7 +13,7 @@ def s3_object_storage_iterator(
     disk: S3DiskConfiguration,
     *,
     object_name_prefix: str = "",
-    skip_ignoring: bool = False
+    skip_ignoring: bool = False,
 ) -> Iterator[ObjectSummary]:
     s3 = boto3.resource(
         "s3",
diff --git a/ch_tools/chadmin/internal/utils.py b/ch_tools/chadmin/internal/utils.py
index 1b362836..894d92e3 100644
--- a/ch_tools/chadmin/internal/utils.py
+++ b/ch_tools/chadmin/internal/utils.py
@@ -1,6 +1,7 @@
 """
 Utility functions.
 """
+
 import re
 import subprocess
 from itertools import islice
diff --git a/ch_tools/common/cli/utils.py b/ch_tools/common/cli/utils.py
index ce030482..030bcde6 100644
--- a/ch_tools/common/cli/utils.py
+++ b/ch_tools/common/cli/utils.py
@@ -36,13 +36,12 @@ def diff_objects(value1, value2):
     """
     Calculate structural diff between 2 values.
     """
-    ignore_type_in_groups = [(dict, defaultdict)]
     return DeepDiff(
         value1,
         value2,
         verbose_level=2,
         view="tree",
-        ignore_type_in_groups=ignore_type_in_groups,
+        ignore_type_in_groups=[(dict, defaultdict)],
     )
 
 
diff --git a/pyproject.toml b/pyproject.toml
index f5795dfe..fd767791 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ readme = "README.md"
 homepage = "https://github.com/yandex/ch-tools"
 repository = "https://github.com/yandex/ch-tools"
 dynamic = ["version"]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 keywords = [
     "clickhouse",
     "database",
@@ -60,9 +60,9 @@ maintainers = [
 ]
 dependencies = [
     "boto3 ~= 1.23.10",
-    "click ~= 8.0.4",
+    "click >= 8.1, < 8.2",
     "cloup",
-    "deepdiff < 6.4.0",
+    "deepdiff >= 8.0, < 9.0",
     "dnspython",
     "file_read_backwards",
     "humanfriendly",
@@ -73,31 +73,27 @@ dependencies = [
     "pygments",
     "pyopenssl < 25.0",
     "python-dateutil",
-    "pyyaml < 5.4",
-    "requests < 2.30",
+    "pyyaml >= 5.4",
+    "requests >= 2.20, < 2.30",
     "tabulate",
     "tenacity",
     "termcolor",
     "tqdm",
-    "typing-extensions ~= 4.1",
     "xmltodict",
     "loguru",
-    "cffi == 1.16.0 ; python_version >= '3.12'",
-    "setuptools ; python_version >= '3.12'",
+    "setuptools >= 71.1",  # for pkg_resources module
 ]
 
 [dependency-groups]
 dev = [
     "behave",
-    "docker < 8.0",
-    "docker-compose < 1.29 ; python_version < '3.13'",
+    "docker >= 4.0",
     "pyhamcrest",
     "pytest",
-    "pyfakefs ; python_version < '3.12'",
-    "pyfakefs == 5.5.0 ; python_version >= '3.12'",
-    "black ~= 22.0",
+    "pyfakefs",
+    "black >= 25.1",
     "ruff",
-    "isort >= 6.0; python_version >= '3.9'",
+    "isort >= 6.0",
     "mypy >= 1.5, < 1.6",
     "pylint >= 3.0, < 4.0",
     "types-pyOpenSSL",
diff --git a/tests/configuration.py b/tests/configuration.py
index 71946f97..dfe1b6c8 100644
--- a/tests/configuration.py
+++ b/tests/configuration.py
@@ -1,6 +1,7 @@
 """
 Variables that influence testing behavior are defined here.
 """
+
 import os
 
 
diff --git a/tests/modules/compose.py b/tests/modules/compose.py
index 0a0f0511..364d7595 100644
--- a/tests/modules/compose.py
+++ b/tests/modules/compose.py
@@ -5,6 +5,7 @@
 import os
 import random
 import shlex
+import shutil
 import subprocess
 
 import docker
@@ -112,7 +113,7 @@ def _validate_config(config_path: str) -> None:
     """
     Perform config validation by calling `docker-compose config`
     """
-    _call_compose_on_config(config_path, "__config_test", "config")
+    _call_compose_on_config(config_path, "config_test", "config")
 
 
 def _generate_compose_config(config: dict) -> dict:
@@ -219,6 +220,10 @@ def _call_compose_on_config(conf_path: str, project_name: str, action: str) -> N
     """
     Execute docker-compose action by invoking `docker-compose`.
     """
-    compose_cmd = f"docker-compose --file {conf_path} -p {project_name} {action}"
+    docker_compose = "docker-compose"
+    if shutil.which(docker_compose) is None:
+        docker_compose = "docker compose"
+
+    compose_cmd = f"{docker_compose} --file {conf_path} -p {project_name} {action}"
     # Note: build paths are resolved relative to config file location.
     subprocess.check_call(shlex.split(compose_cmd))
diff --git a/tests/modules/minio.py b/tests/modules/minio.py
index 9f9d08da..9e2a2d97 100644
--- a/tests/modules/minio.py
+++ b/tests/modules/minio.py
@@ -1,6 +1,7 @@
 """
 Interface to Minio S3 server.
 """
+
 import json
 import os
 
diff --git a/tests/modules/typing.py b/tests/modules/typing.py
index 4d8cefc9..3ea79b63 100644
--- a/tests/modules/typing.py
+++ b/tests/modules/typing.py
@@ -1,6 +1,7 @@
 """
 Type definitions.
 """
+
 from types import SimpleNamespace
 from typing import Union
 
diff --git a/tests/steps/failure_mockers.py b/tests/steps/failure_mockers.py
index 85bc9519..46d58aed 100644
--- a/tests/steps/failure_mockers.py
+++ b/tests/steps/failure_mockers.py
@@ -1,6 +1,7 @@
 """
 Steps for interacting with ClickHouse DBMS.
 """
+
 import os
 
 from behave import when
diff --git a/uv.lock b/uv.lock
index 097bd553..50ba2e52 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,114 +1,24 @@
 version = 1
 revision = 2
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 resolution-markers = [
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     "python_full_version == '3.11.*'",
-    "python_full_version == '3.10.*'",
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-]
-
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+    "python_full_version < '3.11'",
 ]
 
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+    { name = "dnspython" },
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-    { name = "termcolor", version = "3.1.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" },
+    { name = "tenacity" },
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-    { name = "pylint", version = "3.3.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" },
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-    { name = "types-setuptools", version = "80.3.0.20250505", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.9'" },
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-    { name = "cffi", marker = "python_full_version >= '3.12'", specifier = "==1.16.0" },
-    { name = "click", specifier = "~=8.0.4" },
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     { name = "dnspython" },
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-    { name = "requests", specifier = "<2.30" },
-    { name = "setuptools", marker = "python_full_version >= '3.12'" },
+    { name = "pyyaml", specifier = ">=5.4" },
+    { name = "requests", specifier = ">=2.20,<2.30" },
+    { name = "setuptools", specifier = ">=71.1" },
     { name = "tabulate" },
     { name = "tenacity" },
     { name = "termcolor" },
     { name = "tqdm" },
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 [package.metadata.requires-dev]
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-    { name = "black", specifier = "~=22.0" },
+    { name = "black", specifier = ">=25.1" },
     { name = "codespell" },
-    { name = "docker", specifier = "<8.0" },
-    { name = "docker-compose", marker = "python_full_version < '3.13'", specifier = "<1.29" },
-    { name = "isort", marker = "python_full_version >= '3.9'", specifier = ">=6.0" },
+    { name = "docker", specifier = ">=4.0" },
+    { name = "isort", specifier = ">=6.0" },
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-    { name = "pyfakefs", marker = "python_full_version >= '3.12'", specifier = "==5.5.0" },
+    { name = "pyfakefs" },
     { name = "pyhamcrest" },
     { name = "pylint", specifier = ">=3.0,<4.0" },
     { name = "pytest" },
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submitted_at: 2025-05-23T09:24:48Z

Review comments:
diff_hunk: @@ -73,31 +73,27 @@ dependencies = [
     "pygments",
     "pyopenssl < 25.0",
     "python-dateutil",
-    "pyyaml < 5.4",
-    "requests < 2.30",
+    "pyyaml >= 5.4",
+    "requests >= 2.20, < 2.30",
     "tabulate",
     "tenacity",
     "termcolor",
     "tqdm",
-    "typing-extensions ~= 4.1",
     "xmltodict",
     "loguru",
-    "cffi == 1.16.0 ; python_version >= '3.12'",
-    "setuptools ; python_version >= '3.12'",
+    "setuptools >= 71.1",  # for pkg_resources module
path: pyproject.toml
user: login: sourcery-ai[bot]
body: **suggestion (bug_risk):** Unbounded upper version for setuptools

Add an upper version limit to `setuptools` (e.g., `< 80.0`) to avoid issues with future incompatible releases.

```suggestion
    "setuptools >= 71.1, < 80.0",  # for pkg_resources module
```
created_at: 2025-05-22T09:12:27Z
author_association: CONTRIBUTOR
diff_hunk: @@ -73,31 +73,27 @@ dependencies = [
     "pygments",
     "pyopenssl < 25.0",
     "python-dateutil",
-    "pyyaml < 5.4",
-    "requests < 2.30",
+    "pyyaml >= 5.4",
+    "requests >= 2.20, < 2.30",
     "tabulate",
     "tenacity",
     "termcolor",
     "tqdm",
-    "typing-extensions ~= 4.1",
     "xmltodict",
     "loguru",
-    "cffi == 1.16.0 ; python_version >= '3.12'",
-    "setuptools ; python_version >= '3.12'",
+    "setuptools >= 71.1",  # for pkg_resources module
path: pyproject.toml
user: login: Alex-Burmak
body: For protection from future incompatible releases it's used dependency lock file.
created_at: 2025-05-22T09:23:29Z
author_association: MEMBER
diff_hunk: @@ -112,7 +113,7 @@ def _validate_config(config_path: str) -> None:
     """
     Perform config validation by calling `docker-compose config`
     """
-    _call_compose_on_config(config_path, "__config_test", "config")
path: tests/modules/compose.py
user: login: Alex-Burmak
body: `__config_test` is an invalid value in actual versions of Docker Compose:

```
2025-05-22 10:14:10,960 [INFO    ]:	creating new test config
initiating create stage modules.templates.render_docker_configs
2025-05-22 10:14:10,960 [INFO    ]:	initiating create stage modules.templates.render_docker_configs
initiating create stage modules.compose.create_config
2025-05-22 10:14:10,985 [INFO    ]:	initiating create stage modules.compose.create_config
invalid project name "__config_test": must consist only of lowercase alphanumeric characters, hyphens, and underscores as well as start with a letter or number
modules.compose.create_config failed: RuntimeError('Unable to write config: validation failed.')
```
created_at: 2025-05-22T11:52:19Z
author_association: MEMBER

PR comments:
user: login: sourcery-ai[bot]
created_at: 2025-05-22T09:04:37Z
body: <!-- Generated by sourcery-ai[bot]: start review_guide -->

## Reviewer's Guide

This PR modernizes the build and test tooling by introducing explicit checks for UV, Docker, and Docker Compose (v2), updates and relaxes various dependency version constraints in pyproject.toml (including raising the minimum Python version to 3.9), and applies minor code cleanups for consistency in formatting.

#### Flow Diagram: Updated `test-integration` Target Logic

```mermaid
graph TD
    Start("`make test-integration`") --> CheckDC["Target: check-docker-compose"];
    CheckDC --> CheckDocker["Target: check-docker (dependency of check-docker-compose)"];
    CheckDocker -- "Docker available" --> VerifyDC["Check Docker Compose (v1/v2)"];
    CheckDocker -- "Docker NOT available" --> ErrorDocker["Error: Docker not found & Exit"];
    VerifyDC -- "Docker Compose available" --> BuildPkgs["Target: build-python-packages"];
    VerifyDC -- "Docker Compose NOT available" --> ErrorDC["Error: Docker Compose not found & Exit"];
    BuildPkgs --> RunTests["Run integration tests"];
    RunTests --> EndSuccess(("Success"));
    ErrorDocker --> EndFailure(("Failure"));
    ErrorDC --> EndFailure;
```

#### Flow Diagram: Updated `build-deb-package` Target Logic

```mermaid
graph TD
    Start("`make build-deb-package`") --> CheckDocker["Target: check-docker"];
    CheckDocker -- "Docker available" --> SetupTarget["Target: setup"];
    CheckDocker -- "Docker NOT available" --> ErrorDocker["Error: Docker not found & Exit"];

    SetupTarget --> CheckUV["Target: check-uv (new dependency of setup)"];
    CheckUV -- "UV available" --> VersionFile["Generate/Check VERSION_FILE (part of setup)"];
    CheckUV -- "UV NOT available" --> ErrorUV["Error: UV not found & Exit"];

    VersionFile --> BuildDebScript["Execute ./build_deb_in_docker.sh"];
    BuildDebScript --> EndSuccess(("Success"));

    ErrorDocker --> EndFailure(("Failure"));
    ErrorUV --> EndFailure;
```

### File-Level Changes

| Change | Details | Files |
| ------ | ------- | ----- |
| Makefile modernization with explicit tooling checks and Compose v2 support | <ul><li>Added CLICKHOUSE_VERSION variable</li><li>Replaced deprecated check-environment with check-uv</li><li>Introduced check-docker and check-docker-compose targets</li><li>Updated test-integration and build-deb-package dependencies to use new checks</li></ul> | `Makefile` |
| Dependency version bumps and removals in pyproject.toml | <ul><li>Raised requires-python to >=3.9</li><li>Relaxed and updated version bounds for click, deepdiff, pyyaml, requests, setuptools</li><li>Removed deprecated docker-compose v1 and upgraded dev deps (docker>=4.0, black>=25.1, etc.)</li></ul> | `pyproject.toml` |
| Minor code refactors for style consistency | <ul><li>Collapsed multiline assignment in object_storage_group</li><li>Inlined ignore_type_in_groups list in DeepDiff call</li><li>Added trailing comma to s3_iterator function signature</li></ul> | `ch_tools/chadmin/cli/object_storage_group.py`<br/>`ch_tools/common/cli/utils.py`<br/>`ch_tools/chadmin/internal/object_storage/s3_iterator.py` |

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author_association: CONTRIBUTOR
user: login: Alex-Burmak
created_at: 2025-05-22T09:05:09Z
body: Similar changes in ch-backup repo - https://github.com/yandex/ch-backup/pull/234
author_association: MEMBER