Add usage instructions and update dependency handling

pyproject.toml

@@ -4,7 +4,9 @@ build-backend = 'mesonpy'
 requires = [
     'meson-python',
     'cypari2 >=2.1.1',
-    'cysignals >=1.11.4',
+    # cysignals 1.11.2 is the newest version that is available on conda:
+    # https://github.com/conda-forge/cysignals-feedstock/pull/49
+    'cysignals >=1.11.2',
     # Exclude 3.0.3 because of https://github.com/cython/cython/issues/5748
     'cython >=3.0, != 3.0.3',
     'gmpy2 ~=2.1.b999',

tools/README.md

@@ -2,12 +2,28 @@
 
 This folder contains various command-line tools that are used to facilitate different development tasks. Below is a brief description of each command available in this directory.
 
+## Update Conda Environment Files
+
+This command is used to update the Conda environment files in the project. It automatically adds new dependencies to the Conda files, removes deleted dependencies, and updates the version of existing dependencies. The source of the dependencies is the `pyproject.toml` file, which specifies the following dependencies:
+
+- `build-system.requires`: Python dependencies required for building
+- `project.dependencies`: Python dependencies required for running
+- `external.build-requires`: External dependencies required for building
+- `external.host-requires`: External dependencies required for running
+
+
+Within an active virtual environment where `grayskull` and `conda-lock` is installed, run the following command:
+
+```bash
+tools/update-conda.py
+```
+
 ## Update Meson Build Files
 
 This command is used to updates the Meson build files in the project. It automatically adds new source files (py, pyx) to the Meson files and removes deleted source files. This command is useful when adding or removing source files from the project.
 
 Within an active virtual environment where Meson is installed, run the following command:
 
 ```bash
-tools/update_meson.py
+tools/update-meson.py
 ```

tools/update-conda.py

@@ -68,10 +68,10 @@ def update_conda(source_dir: Path) -> None:
 
                 env_file = source_dir / f"environment{tag}-{python}.yml"
                 write_env_file(env_file, pinned_dependencies)
-                lock_file = (
-                    source_dir / f"environment{tag}-{python}-{platform_value}"
+                lock_file = source_dir / f"environment{tag}-{python}-{platform_value}"
+                lock_file_gen = (
+                    source_dir / f"environment{tag}-{python}-{platform_value}.yml"
                 )
-                lock_file_gen = source_dir / f"environment{tag}-{python}-{platform_value}.yml"
                 print(
                     f"Updating lock file for {env_file} at {lock_file_gen}", flush=True
                 )
@@ -94,7 +94,7 @@ def update_conda(source_dir: Path) -> None:
                     ],
                     check=True,
                 )
-                
+
                 # Add conda env name to lock file at beginning
                 with open(lock_file_gen, "r+") as f:
                     content = f.read()
@@ -123,37 +123,33 @@ def get_dependencies(pyproject_toml: Path) -> list[str]:
     all_requirements.append("cxx-compiler")
 
     # Correct pypi name for some packages
-    python_requirements = pyproject_metadata.get("install_requires", [])
+    python_requirements = set(pyproject_metadata.get("install_requires", []))
     # Specify concrete packages for some packages not yet in grayskull
-    # TODO: It seems to be a bug that these external.dependencies are added to install_requires by grayskull
     python_requirements.remove("pkg:generic/tachyon")
-    python_requirements.append("tachyon")
+    python_requirements.add("tachyon")
     python_requirements.remove("pkg:generic/sagemath-elliptic-curves")
-    python_requirements.append("sagemath-db-elliptic-curves")
+    python_requirements.add("sagemath-db-elliptic-curves")
     python_requirements.remove("pkg:generic/sagemath-polytopes-db")
-    python_requirements.append("sagemath-db-polytopes")
-    python_requirements.remove("pkg:generic/sagemath-graphs")
-    python_requirements.append("sagemath-db-graphs")
+    python_requirements.add("sagemath-db-polytopes")
+    python_requirements.discard("pkg:generic/sagemath-graphs")
+    python_requirements.add("sagemath-db-graphs")
+    python_requirements.remove("memory_allocator")
+    python_requirements.add("memory-allocator")
     # Following can be removed once https://github.com/regro/cf-scripts/pull/2176 is used in grayskull
-    python_requirements = [
+    python_requirements = {
         req.replace("lrcalc", "python-lrcalc") for req in python_requirements
-    ]
+    }
     all_requirements += normalize_requirements_list(
         python_requirements, grayskull_config
     )
     all_requirements.remove("<{ pin_compatible('numpy') }}")
-
-    # Add version constraints for some packages (not yet supported by grayskull/PEP 725)
-    all_requirements.remove("c-compiler")
-    all_requirements.append("c-compiler <=1.6")
-    all_requirements.remove("cxx-compiler")
-    all_requirements.append("cxx-compiler <=1.6")
+    all_requirements.remove("memory_allocator")
     return all_requirements
 
 
 def get_dev_dependencies(pyproject_toml: Path) -> list[str]:
     pyproject = tomllib.load(pyproject_toml)
-    dependency_groups = pyproject["dependency-groups"]
+    dependency_groups = pyproject.get("dependency-groups", {})
     dev_dependencies = dependency_groups.get("test", []) + dependency_groups.get(
         "docs", []
     )