pyhermes-cosmo 1.1.0__tar.gz

pyhermes_cosmo-1.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024-2026 PyHermes Team
+
+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.

pyhermes_cosmo-1.1.0/PKG-INFO

@@ -0,0 +1,230 @@
+Metadata-Version: 2.4
+Name: pyhermes-cosmo
+Version: 1.1.0
+Summary: High-performance multiresolution cosmic statistics in Python
+Author-email: PyHermes Team <dingdluan@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://pyhermes.astroslacker.com
+Project-URL: Documentation, https://pyhermes.astroslacker.com
+Project-URL: Repository, https://github.com/SYSUSPA-Projects/PyHermes
+Project-URL: Issues, https://github.com/SYSUSPA-Projects/PyHermes/issues
+Keywords: cosmology,large-scale structure,correlation function,MPI,scientific computing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: h5py
+Requires-Dist: hdf5plugin
+Requires-Dist: json5
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: PyWavelets
+Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: rich
+Requires-Dist: scipy
+Requires-Dist: termcolor>=1.1
+Provides-Extra: mpi
+Requires-Dist: mpi4py>=4; extra == "mpi"
+Provides-Extra: plot
+Requires-Dist: matplotlib>=3.7; extra == "plot"
+Provides-Extra: camb
+Requires-Dist: camb>=1.5; extra == "camb"
+Provides-Extra: docs
+Requires-Dist: ipython-pygments-lexers>=1.1; extra == "docs"
+Requires-Dist: nbsphinx>=0.9; extra == "docs"
+Requires-Dist: nbsphinx-link>=1.4; extra == "docs"
+Requires-Dist: pypandoc-binary>=1.15; extra == "docs"
+Requires-Dist: sphinx>=8; extra == "docs"
+Requires-Dist: pydata-sphinx-theme<0.21,>=0.20; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Provides-Extra: dev
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: ruff>=0.12; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://pyhermes.astroslacker.com/_static/pyhermes_logo_transparent.png" alt="PyHermes logo" width="220">
+</p>
+
+# PyHermes
+
+**PyHermes** is the Python implementation of **Hermes** (HypER-speed
+MultirEsolution cosmic Statistics), an in situ framework for measuring cosmic
+statistics with reusable multiresolution fields and window operators.
+
+A catalogue is projected once into an `SFCField`. Smoothing, geometric binning,
+multipole decomposition, differentiation, and inverse-Laplacian operations are
+then expressed through `WindowFunc` objects. The same field can therefore feed
+counting, 2PCF, conventional 3PCF, 3PCF multipoles, marked statistics, and
+derived physical-field calculations without returning to particle-level tuple
+counting for every configuration.
+
+- **Documentation:** [pyhermes.astroslacker.com](https://pyhermes.astroslacker.com)
+- **Source:** [SYSUSPA-Projects/PyHermes](https://github.com/SYSUSPA-Projects/PyHermes)
+- **Tutorials:** [`examples/notebooks/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/notebooks)
+- **Runnable configurations:** [`examples/configs/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/configs) and
+  [`examples/scripts/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/scripts)
+
+![Hermes field-window workflow](https://pyhermes.astroslacker.com/_static/paper/PyHermes-Workflow.png)
+
+## What It Covers
+
+- catalogue-to-field projection with configurable compactly supported scaling
+  functions and resolution `J`;
+- built-in and user-defined smoothing, binning, multipole, and operator windows;
+- one-point counting and field sampling;
+- isotropic and anisotropic 2PCF measurements;
+- Monte Carlo and spherical-harmonic 3PCF estimators;
+- MPI/thread parallelism and CPU or CUDA contraction for 3PCF multipoles;
+- weighted fields, velocity derivatives, Poisson potential, acceleration, and
+  density-dependent marks.
+
+## Installation
+
+For notebooks, development, and other single-process work, install PyHermes
+from PyPI:
+
+```bash
+python -m pip install pyhermes-cosmo
+```
+
+This installs PyHermes and its regular Python dependencies automatically. MPI
+and CUDA are optional, so neither is required for the default installation.
+
+The Python import name remains unchanged:
+
+```python
+import pyhermes
+```
+
+For a ready-to-use MPICH environment on Linux or macOS:
+
+```bash
+conda create -n pyhermes -c conda-forge python=3.12 mpi4py mpich pip
+conda activate pyhermes
+python -m pip install pyhermes-cosmo
+mpiexec -n 2 python -c "from mpi4py import MPI; print(MPI.COMM_WORLD.rank)"
+```
+
+Here conda provides a mutually compatible MPI runtime and Python binding, while
+pip installs PyHermes and the remaining Python dependencies. PyHermes does not
+yet require a separate conda package for this workflow.
+
+Without `mpi4py`, PyHermes automatically uses its single-process MPI fallback.
+Users of an existing cluster MPI should follow the
+[installation guide](https://pyhermes.astroslacker.com/install.html) for
+the matching `mpi4py` and GPU setup.
+
+## Smallest Workflow
+
+The tracked Quick Start configurations use paths relative to `examples/`:
+
+```bash
+cd examples
+python scripts/run_sfc_projection.py configs/param_sfc_projection.yaml
+python scripts/run_2pcf.py configs/param_2pcf.yaml
+```
+
+The first command downloads and caches the original single-file Quijote
+`group_tab` catalogue from the URL in the YAML, verifies its SHA256 digest,
+and writes the base `SFCField`. The second command consumes that exact field
+and writes an isotropic `Corr2PCFData` result. The matching
+`quick_start.ipynb` executes the same configs and plotting code rather than
+maintaining a parallel example.
+
+The dedicated `particle_io.ipynb` reuses that catalogue and shows how the
+native FoF reader, an NPZ conversion, and a raw BIN layout all feed the same
+projection API. The converted NPZ and BIN files are local teaching products,
+not additional public downloads.
+`sfc_projection.ipynb` then builds the J=9, weighted, redshift-space, and
+explicit sampled-random fields used by later examples;
+`scripts/prepare_sfc_fields.py` provides the equivalent non-interactive batch
+entry point. The optional dark-matter snapshot builder accepts the local
+Gadget HDF5 snapshot prefix explicitly; no cluster-specific path is embedded
+in the code:
+
+```bash
+python scripts/build_quijote_dm_sfc_field.py /path/to/snapdir_004/snap_004
+```
+
+```python
+from pyhermes.base.sfc_projection import SFCProjection
+from pyhermes.io import WindowFunc
+from pyhermes.param.parambase import read_param
+
+params = read_param("./configs/param_sfc_projection.yaml")
+field = SFCProjection(params).run()
+
+gaussian = WindowFunc(
+    {"type": "gaussian", "len_args": {"R": 10.0}},
+    field.sfc_info,
+    threads=8,
+)
+smoothed_field = field @ gaussian
+```
+
+This is the core language of PyHermes: **field @ window**. Statistical tasks
+build the required window families and normalizations around the same objects.
+
+## Start With The Notebooks
+
+The recommended route through
+[`examples/notebooks/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/notebooks)
+is:
+
+1. [`quick_start.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/quick_start.ipynb)
+2. [`particle_io.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/particle_io.ipynb)
+3. [`sfc_projection.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/sfc_projection.ipynb)
+4. [`window.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/window.ipynb)
+5. [`physical_fields.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/physical_fields.ipynb)
+6. [`counting.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/counting.ipynb)
+7. [`corr2pcf.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/corr2pcf.ipynb)
+8. [`corr3pcf.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/corr3pcf.ipynb)
+
+The first four notebooks establish the common catalogue-to-field-to-window
+workflow. Continue with physical fields, one-point Counting, or the
+2PCF-to-3PCF statistics path according to the calculation you need.
+
+Generated catalogues and estimator products are intentionally not committed.
+The notebooks state which lightweight cells run locally and which script/YAML
+pairs are intended for a workstation or cluster.
+
+## Documentation
+
+The full guide at [pyhermes.astroslacker.com](https://pyhermes.astroslacker.com)
+follows the terminology and estimator definitions of the Hermes paper. It
+covers the mathematical construction, current APIs, window catalogue,
+parameter mappings, numerical validation, and performance interpretation.
+
+To build the documentation locally:
+
+```bash
+python -m pip install ".[docs]"
+sphinx-build -W -b html docs docs/_build/html
+```
+
+## Citing PyHermes
+
+If PyHermes contributes to a publication, please cite the software and, once
+available, the accompanying Hermes/PyHermes paper. Citation metadata is
+provided in [`CITATION.cff`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/CITATION.cff),
+with BibTeX examples in the
+[citation guide](https://pyhermes.astroslacker.com/citing.html).
+
+The current citation author list is Long-Long Feng, Tengpeng Xu, Tian-Cheng
+Luan and collaborators. The manuscript entry remains clearly
+marked as a placeholder until its final title, journal, and identifier are
+available.

pyhermes_cosmo-1.1.0/README.md

@@ -0,0 +1,173 @@
+<p align="center">
+  <img src="https://pyhermes.astroslacker.com/_static/pyhermes_logo_transparent.png" alt="PyHermes logo" width="220">
+</p>
+
+# PyHermes
+
+**PyHermes** is the Python implementation of **Hermes** (HypER-speed
+MultirEsolution cosmic Statistics), an in situ framework for measuring cosmic
+statistics with reusable multiresolution fields and window operators.
+
+A catalogue is projected once into an `SFCField`. Smoothing, geometric binning,
+multipole decomposition, differentiation, and inverse-Laplacian operations are
+then expressed through `WindowFunc` objects. The same field can therefore feed
+counting, 2PCF, conventional 3PCF, 3PCF multipoles, marked statistics, and
+derived physical-field calculations without returning to particle-level tuple
+counting for every configuration.
+
+- **Documentation:** [pyhermes.astroslacker.com](https://pyhermes.astroslacker.com)
+- **Source:** [SYSUSPA-Projects/PyHermes](https://github.com/SYSUSPA-Projects/PyHermes)
+- **Tutorials:** [`examples/notebooks/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/notebooks)
+- **Runnable configurations:** [`examples/configs/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/configs) and
+  [`examples/scripts/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/scripts)
+
+![Hermes field-window workflow](https://pyhermes.astroslacker.com/_static/paper/PyHermes-Workflow.png)
+
+## What It Covers
+
+- catalogue-to-field projection with configurable compactly supported scaling
+  functions and resolution `J`;
+- built-in and user-defined smoothing, binning, multipole, and operator windows;
+- one-point counting and field sampling;
+- isotropic and anisotropic 2PCF measurements;
+- Monte Carlo and spherical-harmonic 3PCF estimators;
+- MPI/thread parallelism and CPU or CUDA contraction for 3PCF multipoles;
+- weighted fields, velocity derivatives, Poisson potential, acceleration, and
+  density-dependent marks.
+
+## Installation
+
+For notebooks, development, and other single-process work, install PyHermes
+from PyPI:
+
+```bash
+python -m pip install pyhermes-cosmo
+```
+
+This installs PyHermes and its regular Python dependencies automatically. MPI
+and CUDA are optional, so neither is required for the default installation.
+
+The Python import name remains unchanged:
+
+```python
+import pyhermes
+```
+
+For a ready-to-use MPICH environment on Linux or macOS:
+
+```bash
+conda create -n pyhermes -c conda-forge python=3.12 mpi4py mpich pip
+conda activate pyhermes
+python -m pip install pyhermes-cosmo
+mpiexec -n 2 python -c "from mpi4py import MPI; print(MPI.COMM_WORLD.rank)"
+```
+
+Here conda provides a mutually compatible MPI runtime and Python binding, while
+pip installs PyHermes and the remaining Python dependencies. PyHermes does not
+yet require a separate conda package for this workflow.
+
+Without `mpi4py`, PyHermes automatically uses its single-process MPI fallback.
+Users of an existing cluster MPI should follow the
+[installation guide](https://pyhermes.astroslacker.com/install.html) for
+the matching `mpi4py` and GPU setup.
+
+## Smallest Workflow
+
+The tracked Quick Start configurations use paths relative to `examples/`:
+
+```bash
+cd examples
+python scripts/run_sfc_projection.py configs/param_sfc_projection.yaml
+python scripts/run_2pcf.py configs/param_2pcf.yaml
+```
+
+The first command downloads and caches the original single-file Quijote
+`group_tab` catalogue from the URL in the YAML, verifies its SHA256 digest,
+and writes the base `SFCField`. The second command consumes that exact field
+and writes an isotropic `Corr2PCFData` result. The matching
+`quick_start.ipynb` executes the same configs and plotting code rather than
+maintaining a parallel example.
+
+The dedicated `particle_io.ipynb` reuses that catalogue and shows how the
+native FoF reader, an NPZ conversion, and a raw BIN layout all feed the same
+projection API. The converted NPZ and BIN files are local teaching products,
+not additional public downloads.
+`sfc_projection.ipynb` then builds the J=9, weighted, redshift-space, and
+explicit sampled-random fields used by later examples;
+`scripts/prepare_sfc_fields.py` provides the equivalent non-interactive batch
+entry point. The optional dark-matter snapshot builder accepts the local
+Gadget HDF5 snapshot prefix explicitly; no cluster-specific path is embedded
+in the code:
+
+```bash
+python scripts/build_quijote_dm_sfc_field.py /path/to/snapdir_004/snap_004
+```
+
+```python
+from pyhermes.base.sfc_projection import SFCProjection
+from pyhermes.io import WindowFunc
+from pyhermes.param.parambase import read_param
+
+params = read_param("./configs/param_sfc_projection.yaml")
+field = SFCProjection(params).run()
+
+gaussian = WindowFunc(
+    {"type": "gaussian", "len_args": {"R": 10.0}},
+    field.sfc_info,
+    threads=8,
+)
+smoothed_field = field @ gaussian
+```
+
+This is the core language of PyHermes: **field @ window**. Statistical tasks
+build the required window families and normalizations around the same objects.
+
+## Start With The Notebooks
+
+The recommended route through
+[`examples/notebooks/`](https://github.com/SYSUSPA-Projects/PyHermes/tree/main/examples/notebooks)
+is:
+
+1. [`quick_start.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/quick_start.ipynb)
+2. [`particle_io.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/particle_io.ipynb)
+3. [`sfc_projection.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/sfc_projection.ipynb)
+4. [`window.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/window.ipynb)
+5. [`physical_fields.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/physical_fields.ipynb)
+6. [`counting.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/counting.ipynb)
+7. [`corr2pcf.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/corr2pcf.ipynb)
+8. [`corr3pcf.ipynb`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/examples/notebooks/corr3pcf.ipynb)
+
+The first four notebooks establish the common catalogue-to-field-to-window
+workflow. Continue with physical fields, one-point Counting, or the
+2PCF-to-3PCF statistics path according to the calculation you need.
+
+Generated catalogues and estimator products are intentionally not committed.
+The notebooks state which lightweight cells run locally and which script/YAML
+pairs are intended for a workstation or cluster.
+
+## Documentation
+
+The full guide at [pyhermes.astroslacker.com](https://pyhermes.astroslacker.com)
+follows the terminology and estimator definitions of the Hermes paper. It
+covers the mathematical construction, current APIs, window catalogue,
+parameter mappings, numerical validation, and performance interpretation.
+
+To build the documentation locally:
+
+```bash
+python -m pip install ".[docs]"
+sphinx-build -W -b html docs docs/_build/html
+```
+
+## Citing PyHermes
+
+If PyHermes contributes to a publication, please cite the software and, once
+available, the accompanying Hermes/PyHermes paper. Citation metadata is
+provided in [`CITATION.cff`](https://github.com/SYSUSPA-Projects/PyHermes/blob/main/CITATION.cff),
+with BibTeX examples in the
+[citation guide](https://pyhermes.astroslacker.com/citing.html).
+
+The current citation author list is Long-Long Feng, Tengpeng Xu, Tian-Cheng
+Luan and collaborators. The manuscript entry remains clearly
+marked as a placeholder until its final title, journal, and identifier are
+available.

pyhermes_cosmo-1.1.0/pyhermes/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.1.0"

pyhermes_cosmo-1.1.0/pyhermes/base/__init__.py

@@ -0,0 +1,2 @@
+from ..io.window import WindowFunc
+from .sfc_projection import SFCProjection

pyhermes_cosmo-1.1.0/pyhermes/base/default_params.json

@@ -0,0 +1,36 @@
+{
+	"enable_default_param": true, // do not change this
+	"SFCProjection": {
+		"fin": {
+			"path": "",
+			"format": "bin",
+			"download": {
+				"cache_path": "",
+				"cache_dir": "",
+				"sha256": "",
+				"timeout": 60
+			},
+			"reader_params": {
+				"dtype": "float32",
+				"ncols": 3,
+				"pos_cols": [0, 1, 2],
+				"fields": {}
+			},
+			"catalog_weight_key": null,
+			"field_value_key": null
+		},
+		"particle_pos": null,
+		"catalog_weight": null,
+		"field_value": null,
+		"weight_normalization": "catalog",
+		"box_size": 1000,
+		"J": 8,
+		"wavelet_mode": "db2",
+		"wavelet_level": 10,
+		"phi_resolution": 1024,
+		"save_particle_data": false,
+		"particle_data_path": "",
+		"threads": 1,
+		"fout_path": ""
+	}
+}