Simulate-I

.github/codecov.yml

@@ -5,4 +5,5 @@ coverage:
       default:
         target: 75%
         threshold: 5%
-        if_ci_failed: error
+        if_ci_failed: error
+    patch: off

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v4

.gitignore

@@ -256,11 +256,11 @@ pyrightconfig.json
 
 ### VisualStudioCode ###
 .vscode/*
-!.vscode/settings.json
-!.vscode/tasks.json
-!.vscode/launch.json
-!.vscode/extensions.json
-!.vscode/*.code-snippets
+.vscode/settings.json
+.vscode/tasks.json
+.vscode/launch.json
+.vscode/extensions.json
+.vscode/*.code-snippets
 
 # Local History for Visual Studio Code
 .history/

docs/api/base.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.base
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/block.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.block
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/core.md

@@ -5,7 +5,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.core.stats
    :members:
-   :undoc-members:
    :show-inheritance:
 ```
 
@@ -14,7 +13,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.core.filters
    :members:
-   :undoc-members:
    :show-inheritance:
 ```
 
@@ -23,7 +21,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.core.rfi
    :members:
-   :undoc-members:
    :show-inheritance:
 
 ```
@@ -33,6 +30,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.core.kernels
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/foldedcube.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.foldedcube
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/fourierseries.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.fourierseries
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/header.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.header
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/index.md

@@ -1,10 +1,5 @@
 # sigpyproc
 
-```{eval-rst}
-.. py:module:: sigpyproc
-
-```
-
 ## Subpackages
 
 ```{toctree}

docs/api/io.md

@@ -5,7 +5,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.io.sigproc
    :members:
-   :undoc-members:
    :show-inheritance:
 ```
 
@@ -14,7 +13,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.io.bits
    :members:
-   :undoc-members:
    :show-inheritance:
 ```
 
@@ -23,7 +21,6 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.io.fileio
    :members:
-   :undoc-members:
    :show-inheritance:
 ```
 
@@ -32,6 +29,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.io.pfits
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/params.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.params
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/readers.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.readers
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/timeseries.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.timeseries
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/api/utils.md

@@ -3,6 +3,5 @@
 ```{eval-rst}
 .. automodule:: sigpyproc.utils
    :members:
-   :undoc-members:
    :show-inheritance:
 ```

docs/conf.py

@@ -57,6 +57,7 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "**.ipynb_checkpoints", "Thumbs.db", ".DS_Store"]
+default_role = "any"
 
 rst_epilog = f"""
 .. |project| replace:: {project}
@@ -84,14 +85,17 @@
 autodoc_member_order = "bysource"
 autodoc_typehints = "none"
 
-numpydoc_show_class_members = False
+numpydoc_show_class_members = True
 numpydoc_show_inherited_class_members = False
 numpydoc_class_members_toctree = False
 numpydoc_xref_param_type = True
 numpydoc_xref_aliases = {
     "ndarray": "numpy.ndarray",
     "dtype": "numpy.dtype",
     "ArrayLike": "numpy.typing.ArrayLike",
+    "NDArray": "numpy.typing.NDArray",
+    "float32": "numpy.float32",
+    "complex64": "numpy.complex64",
     "Figure": "matplotlib.figure.Figure",
     "scipy": "scipy",
     "astropy": "astropy",
@@ -130,6 +134,7 @@
     "astropy": ("https://docs.astropy.org/en/stable/", None),
     "attrs": ("https://www.attrs.org/en/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
+    "pyfftw": ("https://pyfftw.readthedocs.io/en/latest/", None),
     "typing_extensions": ("https://typing-extensions.readthedocs.io/en/stable/", None),
 }
 

docs/dev.md

@@ -1,51 +1,52 @@
-(dev)=
-
 # Developer documentation
 
 Here we will cover all the steps required to add new functionality to the
 `sigpyproc` package. To do this, we will first consider adding a new function
-to the {class}`~sigpyproc.base.Filterbank` class.
+to the {py:class}`~sigpyproc.base.Filterbank` class.
 
 ## Adding a new function: `bandpass()`
 
-**Aim:** Add a new function called bandpass, which will return the total power
-as a function of frequency for our observation.
+**Aim:** Add a new function called `bandpass`, which will return the total power
+as a function of frequency for the filterbank data.
 
 **Files to be modified:** `sigpyproc/base.py`, `sigpyproc/core/kernels.py`.
 
 ### Step 1: Write the API part
 
-The first step is to write the user API of the function. As this function
-will run on data with both time and frequency resolution,
-it belongs in the {class}`~sigpyproc.base.Filterbank` class.
+The first step is to write the user API of the function. As this function will run on
+data with both time and frequency resolution, it belongs in the
+{py:class}`~sigpyproc.base.Filterbank` class.
 
 ```python
-def bandpass(self, gulp=512, **kwargs):
+def bandpass(self, gulp=16384, **plan_kwargs):
     bpass_ar = np.zeros(self.header.nchans, dtype=np.float32)
     num_samples = 0
     for nsamps, ii, data in self.read_plan(**plan_kwargs):
-        kernel.extract_bpass(data, bpass_ar, self.header.nchans, nsamps)
+        kernels.extract_bpass(data, bpass_ar, self.header.nchans, nsamps)
         num_samples += nsamps
-    bpass_ar = bpass_ar / num_samples
-    return TimeSeries(bpass_ar, self.header.new_header({"nchans": 1}))
+    bpass_ar /= num_samples
+    hdr_changes = {"nchans": 1, "nsamples": len(bpass_ar)}
+    return TimeSeries(bpass_ar, self.header.new_header(hdr_changes))
 ```
 
-Looking at the important lines, we have:
-Return an instance of the {class}`~sigpyproc.timeseries.TimeSeries` class.
-The {class}`~sigpyproc.timeseries.TimeSeries` class takes two arguments,
-an instance of {py:obj}`numpy.ndarray` and an instance of
-{class}`~sigpyproc.header.Header`.
-
-Now we have something similar to a normal {py:obj}`numpy.ndarray`,
-which exports several other methods for convenience.
+Looking at the important lines, we have returned an instance of the
+{py:class}`~sigpyproc.timeseries.TimeSeries` class.
+The {py:class}`~sigpyproc.timeseries.TimeSeries` class takes two arguments, an instance
+of {py:obj}`numpy.ndarray` and an instance of {py:class}`~sigpyproc.header.Header`.
+It exposes several other methods for convenience.
 
 ### Step 2: Write the core Numba kernel
 
 We called a kernel function named `extract_bpass`. This function belongs in the
-`sigpyproc/core/kernels.py` file. In `kernels.py`, our function looks like:
+`sigpyproc/core/kernels.py` file. The function looks like:
 
 ```python
-@njit(["void(u1[:], f4[:], i4, i4)", "void(f4[:], f4[:], i4, i4)"], cache=True, parallel=True)
+@njit(
+    ["void(u1[:], f4[:], i4, i4)", "void(f4[:], f4[:], i4, i4)"],
+    cache=True,
+    parallel=True,
+    fastmath=True,
+)
 def extract_bpass(inarray, outarray, nchans, nsamps):
     for ichan in prange(nchans):
         for isamp in range(nsamps):
@@ -57,9 +58,10 @@ We use the jit compiler directive `parallel` to enable OpenMP threading.
 
 ## Reporting an issue
 
-[Post an issue on the GitHub repository](https://github.com/FRBs/sigpyproc3/issues). When you post an issue,
-please provide the details to reproduce the issue.
+[Post an issue on the GitHub repository](https://github.com/FRBs/sigpyproc3/issues).
+When you post an issue, please provide the details to reproduce the issue.
 
 ## Contributing code or documentation
 
-An excellent place to start is the [AstroPy developer docs](https://docs.astropy.org/en/stable/development/workflow/development_workflow.html).
+An excellent place to start is the
+[AstroPy developer docs](https://docs.astropy.org/en/stable/development/workflow/development_workflow.html).

docs/modules.md

@@ -1,7 +1,7 @@
 # API Reference
 
 ```{toctree}
-:titlesonly: true
+:titlesonly:
 
 api/index
 ```

docs/tutorials/quickstart.ipynb

@@ -12,7 +12,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Getting started"
+    "# Getting started"
    ]
   },
   {
@@ -26,7 +26,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Loading data into sigpyproc"
+    "## Loading data into sigpyproc"
    ]
   },
   {
@@ -257,7 +257,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Dedispersing the data"
+    "## Dedispersing the data"
    ]
   },
   {
@@ -459,7 +459,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Performing a Fourier transform"
+    "## Performing a Fourier transform"
    ]
   },
   {
@@ -693,7 +693,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Folding data"
+    "## Folding data"
    ]
   },
   {
@@ -822,7 +822,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Tips and tricks"
+    "## Tips and tricks"
    ]
   },
   {
@@ -1015,7 +1015,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,