nautilus-astrochem-code 2.1.0__tar.gz

nautilus_astrochem_code-2.1.0/.codespell.toml

@@ -0,0 +1,3 @@
+[tool.codespell]
+ignore-words-list = 'blanck,inout,INOUT,indext,DELT,fillin,YHE,activ,ACTIV,fonction,ans,oint,te,composant'
+skip              = 'subprojects/**'

nautilus_astrochem_code-2.1.0/.fortitude.toml

@@ -0,0 +1,24 @@
+[check]
+line-length    = 300
+preview        = true
+extend-exclude = [
+  'tests',
+  'subprojects',
+  'src/nautilus_major_reactions.f90',
+  'src/nautilus_rates.f90',
+  'src/nautilus_outputs.f90',
+  'src/nautilus_select_outputs.f90',
+  'src/nautilus_trace_major.f90',
+]
+# uvx --from fortitude-lint@latest fortitude explain S241
+ignore         = [
+  'S241',                              # [quotes]()
+  'C051',                              # [trailing backslash]()
+  'C091',                              # [external procedure](https://fortitude.readthedocs.io/en/stable/rules/external-procedure/#external-procedure-c091)
+  'C121',                              # [use stmt](https://fortitude.readthedocs.io/en/stable/rules/use-all/#use-all-c121)
+  'C131',                              # [accessibility statement](https://fortitude.readthedocs.io/en/stable/rules/missing-accessibility-statement/)
+  'C181',                              # [unchecked-stat](https://fortitude.readthedocs.io/en/stable/rules/unchecked-stat/#unchecked-stat-c181)
+]
+
+[check.strings]
+quotes = 'single'

nautilus_astrochem_code-2.1.0/.fprettify.yaml

@@ -0,0 +1,17 @@
+---
+whitespace-comma: true
+whitespace-plusminus: 1
+whitespace-multdiv: 0
+
+strip-comments: true
+enable-decl: true
+enable-replacements: true
+c-relations: true
+
+# keywords, procedures/modules, operators and constants
+case: [1, 1, 1, 0] # 0: do nothing | 1:lowercase | 2: uppercase
+
+indent: 3
+line-length: 300
+
+exclude: subprojects/*

nautilus_astrochem_code-2.1.0/.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.3
+    hooks:
+      - id: codespell
+        args: [ --toml, .codespell.toml ]
+
+  # Fortran
+  - repo: https://github.com/PlasmaFAIR/fortitude-pre-commit
+    rev: v0.9.2
+    hooks:
+      - id: fortitude
+        args: [ '--config-file=.fortitude.toml', '--fix' ]
+  - repo: https://github.com/fortran-lang/fprettify
+    rev: v0.3.7
+    hooks:
+      - id: fprettify
+        args: [ '-c', '.fprettify.yaml', '-r', 'nautilus-astrochem-code/src' ]
+  - repo: https://github.com/trim21/pre-commit-mirror-meson
+    rev: v1.12.0
+    hooks:
+      - id: meson-fmt
+        args: [ '--inplace', '--recursive' ]
+      - id: meson-fmt
+        args: [ '--check-only', '--recursive' ]

nautilus_astrochem_code-2.1.0/LICENSE

@@ -0,0 +1,28 @@
+The nautilus gas-grain code has been developed at the ''Laboratoire d'astrophysique de Bordeaux''
+by a group of researchers led by Valentine Wakelam from the original code of Eric Herbst (Hasegawa et al. 1992).
+
+Copyright is protected by the following license:
+
+'''MIT License
+Copyright (c) 2016 Valentine Wakelam
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE.'''
+
+When publishing results obtained with nautilus (and any modified version of it), the authors should include the reference:
+''Ruaud et al.~Monthly Notices of the Royal Astronomical Society, Volume 459, Issue 4, p.3756-3767.''
+
+'''If we provide the code for external users of the group, we do not provide any user support.
+If users want help, then they can contact us, but this will be done in the context of a collaboration.'''

nautilus_astrochem_code-2.1.0/PKG-INFO

@@ -0,0 +1,74 @@
+Metadata-Version: 2.4
+Name: nautilus-astrochem-code
+Version: 2.1.0
+Summary: Fortran simulation binaries for the NAUTILUS gas-grain chemistry code
+Author-Email: Valentine Wakelam <valentine.wakelam@u-bordeaux.fr>, Alexandre Mechineau <alexandre.mechineau@u-bordeaux.fr>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Fortran
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: tyro>=1.0.15
+Description-Content-Type: text/markdown
+
+# Nautilus gas-grain code for astrochemistry
+
+![Stable Version](https://img.shields.io/pypi/v/nautilus_astrochem_code?style=for-the-badge&label=Stable)
+![Python Versions](https://img.shields.io/pypi/pyversions/nautilus_astrochem_code?style=for-the-badge&label=Python)
+
+> Python CLI for the Nautilus gas-grain astrochemistry code.
+
+[![](https://img.shields.io/badge/doc-Users-green?style=for-the-badge)](https://lab.pages.in2p3.fr/astrochem-tools/nautilus-doc/ "Science & Examples")
+[![](https://img.shields.io/badge/doc-IN2P3-green?style=for-the-badge)](https://lab.pages.in2p3.fr/astrochem-tools/pnautilus "Public documentation")
+[![](https://img.shields.io/badge/doc-Framagit-grey?style=for-the-badge)](https://wakelam.frama.io/nautilus "Private documentation")
+
+This package is part of the [Nautilus](https://gitlab.in2p3.fr/LAB/astrochem-tools/pnautilus) project.
+
+It provides the compiled Fortran binaries of
+the [Nautilus gas-grain code](https://gitlab.in2p3.fr/LAB/astrochem-tools/pnautilus/-/tree/main/nautilus-astrochem-code)
+for astrochemistry: `nautilus_code` and `nautilus_rates_netcdf`.
+
+> [!important]
+> You are not meant to call these binaries directly.
+> Install the [nautilus-astrochem](https://pypi.org/project/nautilus-astrochem) package instead:
+> it drives these binaries and adds plotting and post-processing.
+
+## Getting started
+
+To get started with `nautilus-astrochem-code`, we offer a repository
+[nautilus-doc](https://gitlab.in2p3.fr/LAB/astrochem-tools/nautilus-doc),
+with scientific documentation and examples of use cases ready to run.
+This repository is used to provide the [documentation website](https://lab.pages.in2p3.fr/astrochem-tools/nautilus-doc/),
+where the content of the documentation is available.
+
+## Installation
+
+This package is a dependency of `nautilus-astrochem`; you normally install it through that
+package rather than on its own.
+
+### Common issues
+
+We provide pre-built wheels for the most common platforms.
+When no wheel matches your platform, or if you force a build from the source,
+the binaries are compiled during installation, so you must provide:
+
+- a Fortran compiler, and
+- the netcdf library for Fortran.
+
+Only `gfortran` with `netcdf-fortran` is tested for now.
+
+- on macOS: `sudo port install gcc14 netcdf-fortran` or `brew install gcc netcdf-fortran`
+- on Ubuntu: `apt install gfortran libnetcdff-dev`
+
+## Contact
+
+Requests or questions can be sent to valentine.wakelam@u-bordeaux.fr.

nautilus_astrochem_code-2.1.0/Readme.md

@@ -0,0 +1,52 @@
+# Nautilus gas-grain code for astrochemistry
+
+![Stable Version](https://img.shields.io/pypi/v/nautilus_astrochem_code?style=for-the-badge&label=Stable)
+![Python Versions](https://img.shields.io/pypi/pyversions/nautilus_astrochem_code?style=for-the-badge&label=Python)
+
+> Python CLI for the Nautilus gas-grain astrochemistry code.
+
+[![](https://img.shields.io/badge/doc-Users-green?style=for-the-badge)](https://lab.pages.in2p3.fr/astrochem-tools/nautilus-doc/ "Science & Examples")
+[![](https://img.shields.io/badge/doc-IN2P3-green?style=for-the-badge)](https://lab.pages.in2p3.fr/astrochem-tools/pnautilus "Public documentation")
+[![](https://img.shields.io/badge/doc-Framagit-grey?style=for-the-badge)](https://wakelam.frama.io/nautilus "Private documentation")
+
+This package is part of the [Nautilus](https://gitlab.in2p3.fr/LAB/astrochem-tools/pnautilus) project.
+
+It provides the compiled Fortran binaries of
+the [Nautilus gas-grain code](https://gitlab.in2p3.fr/LAB/astrochem-tools/pnautilus/-/tree/main/nautilus-astrochem-code)
+for astrochemistry: `nautilus_code` and `nautilus_rates_netcdf`.
+
+> [!important]
+> You are not meant to call these binaries directly.
+> Install the [nautilus-astrochem](https://pypi.org/project/nautilus-astrochem) package instead:
+> it drives these binaries and adds plotting and post-processing.
+
+## Getting started
+
+To get started with `nautilus-astrochem-code`, we offer a repository
+[nautilus-doc](https://gitlab.in2p3.fr/LAB/astrochem-tools/nautilus-doc),
+with scientific documentation and examples of use cases ready to run.
+This repository is used to provide the [documentation website](https://lab.pages.in2p3.fr/astrochem-tools/nautilus-doc/),
+where the content of the documentation is available.
+
+## Installation
+
+This package is a dependency of `nautilus-astrochem`; you normally install it through that
+package rather than on its own.
+
+### Common issues
+
+We provide pre-built wheels for the most common platforms.
+When no wheel matches your platform, or if you force a build from the source,
+the binaries are compiled during installation, so you must provide:
+
+- a Fortran compiler, and
+- the netcdf library for Fortran.
+
+Only `gfortran` with `netcdf-fortran` is tested for now.
+
+- on macOS: `sudo port install gcc14 netcdf-fortran` or `brew install gcc netcdf-fortran`
+- on Ubuntu: `apt install gfortran libnetcdff-dev`
+
+## Contact
+
+Requests or questions can be sent to valentine.wakelam@u-bordeaux.fr.

nautilus_astrochem_code-2.1.0/meson.build

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+project(
+  'Nautilus',
+  ['fortran', 'c'],
+version : '2.1.0',
+  default_options : ['b_pie=true', 'b_lto=true', 'b_lto_mode=thin', 'warning_level=3', 'default_library=static'],
+  meson_version : '>=1.9'
+)
+meson.add_dist_script('version.sh', 'set-dist', meson.project_version())
+
+
+# Common flags to optimize used by both, `nautilus` and `opkd`
+# -ffast-math -finit-real=nan
+## Flags recommended by maqao
+# -funroll-loops -march=native
+
+fc = meson.get_compiler('fortran')
+if fc.get_id() == 'gcc'
+    arg = '-ffree-line-length-0'
+    if fc.has_argument(arg)
+        add_project_arguments(arg, language: 'fortran')
+    endif
+
+    add_project_arguments('-fimplicit-none', language: 'fortran')
+endif
+
+if fc.get_id() == 'intel'
+    args = []
+    args += ['-diag-disable=10448']
+    args += ['-Qparallel']
+
+    add_project_arguments(args, language: 'fortran')
+    add_project_link_arguments(args, language: 'fortran')
+endif
+
+# Use vendored package.
+opkd_sp = subproject('opkd')
+opkd_dep = opkd_sp.get_variable('opkd_dep')
+
+if get_option('verify')
+    warning('Check memory and float operations')
+    add_project_arguments(
+        [
+            '-fcheck=all',
+            '-fbounds-check',
+            '-fstack-protector-all',
+            '-fno-omit-frame-pointer',
+            '-fbacktrace',
+        ],
+        language: 'fortran',
+    )
+    add_project_arguments(
+        [
+            '-finit-real=snan',
+            '-ffpe-trap=invalid,zero,overflow',
+        ],
+        language: 'fortran',
+    )
+endif
+
+# add python package
+subdir('nautilus_astrochem_code')
+# add fortran source
+subdir('src')
+
+
+# add doxygen doc
+fs = import('fs')
+
+if fs.exists('doc/meson.build')
+    subdir('doc')
+endif

nautilus_astrochem_code-2.1.0/meson.options

@@ -0,0 +1,27 @@
+option(
+    'verify',
+    type: 'boolean',
+    value: false,
+    description: 'Enable extra Fortran runtime/debug checks',
+)
+
+option(
+    'enable_python',
+    type: 'boolean',
+    value: false,
+    description: 'Build the python package',
+)
+
+option(
+    'enable_doxygen',
+    type: 'boolean',
+    value: false,
+    description: 'Build the doxygen documentation',
+)
+
+option(
+    'enable_ascii_binaries',
+    type: 'boolean',
+    value: true,
+    description: 'Build the binary for the original ASCII format',
+)

nautilus_astrochem_code-2.1.0/nautilus_astrochem_code/__init__.py

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+"""
+Provides access to the `nautilus_code` and `nautilus_rates` command.
+Also expose their input class.
+
+User should not need to import anything from this module or its submodules.
+"""
+
+from .binaries.nautilus_code import NautilusCode, nautilus_code
+from .binaries.nautilus_rates import NautilusRates, nautilus_rates
+
+__all__ = ('NautilusCode', 'NautilusRates', 'nautilus_code', 'nautilus_rates')

nautilus_astrochem_code-2.1.0/nautilus_astrochem_code/binaries/binary.py

@@ -0,0 +1,135 @@
+from __future__ import annotations
+
+import os
+from contextlib import contextmanager
+from typing import TYPE_CHECKING, Literal, NoReturn, assert_never, overload
+
+from loguru import logger
+
+if TYPE_CHECKING:
+    from collections.abc import Generator
+    from pathlib import Path
+    from subprocess import CompletedProcess
+
+__all__ = ('NautilusBinary', 'get_nautilus_binary', 'invoke_binary')
+
+NautilusBinary = Literal['nautilus_code', 'nautilus_rates', 'nautilus_rates_netcdf']
+"""Available binaries from the nautilus astrochemistry code."""
+
+NautilusAsciiBinary = Literal[
+    'nautilus_outputs', 'nautilus_select_outputs', 'nautilus_major_reactions', 'nautilus_trace_major'
+]
+
+
+def get_version() -> str:
+    """Get the version of the package."""
+    import importlib.metadata
+
+    return importlib.metadata.version('nautilus-astrochem-code')
+
+
+def get_sideloaded_nautilus_binary(binary_name: NautilusBinary | NautilusAsciiBinary, build_dir: Path) -> Path:
+    logger.warning(f'Sideloading `{binary_name}` -> {build_dir} [from NAUTILUS_ASTROCHEM_BUILD_DIR]')
+
+    bin_path = build_dir / 'src' / binary_name
+
+    if not bin_path.is_file():
+        msg = f'`NAUTILUS_ASTROCHEM_BUILD_DIR` set to `{build_dir}`, but `{bin_path}` was not found.'
+        raise FileNotFoundError(msg)
+
+    if not os.access(bin_path, os.X_OK):
+        bin_path.chmod(0o755)
+
+    return bin_path
+
+
+@contextmanager
+def get_nautilus_binary(
+    binary_name: NautilusBinary | NautilusAsciiBinary, *, allow_sideload: bool = False
+) -> Generator[Path]:
+    """Get the path to a nautilus binary.
+
+    If `allow_sideload` is set and `NAUTILUS_ASTROCHEM_BUILD_DIR` is set, sideload the binary
+    from that user-managed meson build directory, instead of the one bundled in the package.
+     Useful during development to pick up a Fortran rebuild without reinstalling the python package.
+
+    `allow_sideload` is only ever set by `nautilus_astrochem_code`'s own CLI entrypoints: downstream
+    consumers are unable to enable it, so their users cannot sideload binaries regardless
+    of environment variables set on their machine.
+
+    Otherwise, fall back to the binary bundled with the package.
+    Log the path and version of the binary.
+    """
+    from pathlib import Path
+
+    # Fast path: if sideload is allowed and build dir is set, use that
+    if allow_sideload is True and (build_dir := os.getenv('NAUTILUS_ASTROCHEM_BUILD_DIR')) is not None:
+        yield get_sideloaded_nautilus_binary(binary_name, Path(build_dir))
+        return
+
+    from importlib import resources
+
+    binary = resources.files(__package__).joinpath(binary_name)
+    with resources.as_file(binary) as bin_path:
+        if not os.access(bin_path, os.X_OK):
+            bin_path.chmod(0o755)
+
+        logger.debug(f'Using `{binary_name}` -> {bin_path} [{get_version()}]')
+        yield bin_path
+
+
+@overload
+def invoke_binary(
+    binary_name: NautilusBinary | NautilusAsciiBinary,
+    args: list[str],
+    *,
+    dry: bool,
+    use_subprocess: Literal[True],
+    allow_sideload: bool,
+) -> CompletedProcess[str]: ...
+
+
+@overload
+def invoke_binary(
+    binary_name: NautilusBinary | NautilusAsciiBinary,
+    args: list[str],
+    *,
+    dry: bool,
+    use_subprocess: Literal[False],
+    allow_sideload: bool,
+) -> NoReturn: ...
+
+
+def invoke_binary(
+    binary_name: NautilusBinary | NautilusAsciiBinary,
+    args: list[str],
+    *,
+    dry: bool,
+    use_subprocess: bool,
+    allow_sideload: bool = False,
+) -> CompletedProcess[str]:
+    """Allow invoking a binary matching `NautilusBinary | NautilusAsciiBinary` with its arguments.
+
+    The other flags allow controlling the invocations.
+    """
+    import subprocess  # ruff: ignore[suspicious-subprocess-import]
+    import sys
+
+    with get_nautilus_binary(binary_name, allow_sideload=allow_sideload) as bin_path:
+        logger.debug(f'With: {args}')
+        bin_str = str(bin_path)
+
+        match use_subprocess:
+            case True:
+                if dry is True:
+                    return subprocess.CompletedProcess(args=[bin_str, *args], returncode=0)
+
+                return subprocess.run([bin_str, *args], capture_output=False, text=True, check=True)  # ruff: ignore[subprocess-without-shell-equals-true]
+            case False:
+                if dry is True:
+                    return sys.exit(0)
+                # replace this process rather than spawning a child:
+                # correct exit code, correct signal forwarding (Ctrl+C, SIGTERM), no double process
+                return os.execv(bin_str, [bin_str, *args])  # ruff: ignore[start-process-with-no-shell]
+            case _:
+                assert_never(use_subprocess)

nautilus_astrochem_code-2.1.0/nautilus_astrochem_code/binaries/nautilus_ascii.py

@@ -0,0 +1,9 @@
+from __future__ import annotations
+
+import sys
+
+from .binary import NautilusAsciiBinary, invoke_binary
+
+
+def nautilus_ascii_binary(binary: NautilusAsciiBinary, *, allow_sideload: bool = False):
+    invoke_binary(binary, sys.argv[1:], dry=False, use_subprocess=False, allow_sideload=allow_sideload)

nautilus_astrochem_code-2.1.0/nautilus_astrochem_code/binaries/nautilus_code.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Annotated
+
+import tyro
+
+
+def nautilus_code(
+    p: Annotated[NautilusCode, tyro.conf.arg(name='')],
+) -> None:
+    """Call `nautilus_code`."""
+    from loguru import logger
+
+    from .binary import invoke_binary
+    from .utils import check_network_present, check_output_file_not_locked
+
+    p.load_env()
+    logger.debug(p)
+
+    if not (parameters := p.parameters).is_file():
+        msg = f'Parameters file not found: `{parameters}`'
+        raise FileNotFoundError(msg)
+
+    if not (abundances := p.abundances).is_file():
+        msg = f'Abundances file not found: `{abundances}`'
+        raise FileNotFoundError(msg)
+
+    # Ensure directory exists and files present.
+    check_network_present(p.network)
+
+    logger.info(f'Using abundances file at: `{abundances}`.')
+    logger.info(f'Using parameters file at: `{parameters}`.')
+    logger.info(f'Using network directory at: `{p.network}`.')
+
+    if (structure_evolution := p.structure_evolution) is not None:
+        if not structure_evolution.is_file():
+            msg = f'Structure evolution file not found: `{structure_evolution}`.'
+            raise FileNotFoundError(msg)
+
+        logger.info(f'Using structure evolution file at: `{structure_evolution}`.')
+
+    if p.ascii is False:
+        # check that there is no lock on the output file
+        check_output_file_not_locked(p.output)
+
+        logger.info(f'Using output file at: `{p.output}`.')
+
+    invoke_binary(
+        'nautilus_code',
+        p.as_cmd_list(),
+        dry=p.dry,
+        use_subprocess=p.subprocess,
+        allow_sideload=p._allow_sideload,  # pyright: ignore[reportPrivateUsage]  # ruff: ignore[private-member-access]
+    )
+
+
+OutputMode = tyro.conf.create_mutex_group(required=False, title='output mode')
+SpatialMode = tyro.conf.create_mutex_group(required=False, title='`0D+T` or `1D`')
+
+
+@dataclass
+class NautilusCode:
+    """Invoke `nautilus_code`."""
+
+    abundances: Path = Path('abundances.in')
+    """Path to an abundances file"""
+    parameters: Path = Path('parameters.in')
+    """Path to a parameters file"""
+
+    network: Path = Path()
+    """Optional path to a network directory"""
+
+    structure_evolution: Annotated[Path | None, SpatialMode, tyro.conf.DisallowNone] = None
+    """Optional path to a structure evolution file"""
+    oneD_static: Annotated[Path | None, SpatialMode, tyro.conf.arg(name='1D-static'), tyro.conf.DisallowNone] = None  # ruff: ignore[mixed-case-variable-in-class-scope]
+    """Optional path to a 1D static file"""
+
+    output: Annotated[Path, OutputMode, tyro.conf.arg(aliases=['-o'])] = Path('output.nc')
+    """Path of the netCDF output file (ignored in ascii mode)  [env: NAUTILUS_ASTROCHEM_OUTPUT]"""
+
+    ascii: Annotated[bool, OutputMode, tyro.conf.FlagCreatePairsOff] = False
+    """Force the output to use ASCII [env: NAUTILUS_ASTROCHEM_ASCII]"""
+
+    dry: Annotated[bool, tyro.conf.FlagCreatePairsOff] = False
+    subprocess: tyro.conf.Suppress[bool] = True
+    _allow_sideload: tyro.conf.Suppress[bool] = False
+    """Internal attributes to allow sideloading the binary."""
+
+    def load_env(self):
+        """Load environment variables."""
+        import os
+
+        if (output := os.getenv('NAUTILUS_ASTROCHEM_OUTPUT')) is not None:
+            self.output = Path(output)
+
+        if (ascii := os.getenv('NAUTILUS_ASTROCHEM_ASCII')) is not None:  # ruff: ignore[builtin-variable-shadowing]
+            self.ascii = bool(ascii)
+
+        if (dry := os.getenv('NAUTILUS_ASTROCHEM_DRY')) is not None:
+            self.dry = bool(dry)
+
+    def as_cmd_list(self) -> list[str]:
+        args = (
+            f'--parameters={self.parameters}',
+            f'--abundances={self.abundances}',
+            f'--network={self.network}',
+            f'--structure-evolution={struct_evol}' if (struct_evol := self.structure_evolution) else None,
+            f'--1D-static={one_d_static} ' if (one_d_static := self.oneD_static) else None,
+            f'--output={self.output}' if self.ascii is False else None,
+        )
+        return list(filter(None, args))

nautilus_astrochem_code-2.1.0/nautilus_astrochem_code/binaries/nautilus_rates.py

@@ -0,0 +1,75 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Annotated
+
+import tyro
+from loguru import logger
+
+
+def nautilus_rates(p: Annotated[NautilusRates, tyro.conf.arg(name='')]):
+    """Call `nautilus_rates`."""
+    from .binary import invoke_binary
+    from .utils import check_output_file_exists, check_output_file_not_locked
+
+    p.load_env()
+    logger.debug(p)
+
+    match p.ascii:
+        case True:
+            invoke_binary(
+                'nautilus_rates',
+                p.as_cmd_list(),
+                dry=p.dry,
+                use_subprocess=p.subprocess,
+                allow_sideload=p._allow_sideload,  # ruff: ignore[private-member-access]  # pyright: ignore[reportPrivateUsage]
+            )
+        case False:
+            check_output_file_exists(p.output)
+            # check that there is no lock on the output file
+            check_output_file_not_locked(p.output)
+
+            logger.info(f'Using output file at: `{p.output}`.')
+
+            invoke_binary(
+                'nautilus_rates_netcdf',
+                p.as_cmd_list(),
+                dry=p.dry,
+                use_subprocess=p.subprocess,
+                allow_sideload=p._allow_sideload,  # ruff: ignore[private-member-access]  # pyright: ignore[reportPrivateUsage]
+            )
+
+
+OutputMode = tyro.conf.create_mutex_group(required=False, title='output mode')
+
+
+@dataclass
+class NautilusRates:
+    output: Annotated[Path, OutputMode, tyro.conf.arg(aliases=['-o'])] = Path('output.nc')
+    """Path of the netCDF file, used as input and output (ignored in ascii mode)  [env: NAUTILUS_ASTROCHEM_OUTPUT]"""
+
+    ascii: Annotated[bool, OutputMode, tyro.conf.FlagCreatePairsOff] = False
+    """Force the output to use ASCII [env: NAUTILUS_ASTROCHEM_ASCII]"""
+
+    dry: Annotated[bool, tyro.conf.FlagCreatePairsOff] = False
+    subprocess: tyro.conf.Suppress[bool] = True
+    _allow_sideload: tyro.conf.Suppress[bool] = False
+    """Internal attributes to allow sideloading the binary."""
+
+    def load_env(self):
+        """Load environment variables."""
+        import os
+
+        if (output := os.getenv('NAUTILUS_ASTROCHEM_OUTPUT')) is not None:
+            self.output = Path(output)
+
+        if (ascii := os.getenv('NAUTILUS_ASTROCHEM_ASCII')) is not None:  # ruff: ignore[builtin-variable-shadowing]
+            self.ascii = bool(ascii)
+
+        if (dry := os.getenv('NAUTILUS_ASTROCHEM_DRY')) is not None:
+            self.dry = bool(dry)
+
+    def as_cmd_list(self) -> list[str]:
+        args = (f'{self.output.as_posix()}' if self.ascii is False else None,)
+        return list(filter(None, args))