Fix module not found (#172)

* Convert to src style package from flat * Update robinhood path for src structure * Bump version, modify changelog * Update README
scikit-tda · Jul 12, 2024 · 59610da · 59610da
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diff --git a/.github/workflows/build_and_deploy.yml b/.github/workflows/build_and_deploy.yml
@@ -20,7 +20,7 @@ jobs:
 
       - name: Clone robinhood
         run: |
-          git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
+          git clone https://github.com/martinus/robin-hood-hashing robinhood
 
       - name: Build wheels
         uses: pypa/[email protected]
@@ -41,7 +41,7 @@ jobs:
 
       - name: Clone robinhood
         run: |
-          git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
+          git clone https://github.com/martinus/robin-hood-hashing robinhood
 
       - name: Build sdist
         run: pipx run build --sdist

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,8 @@
+# 0.6.9
+
+    - Convert package to `src` style.
+    - Fix build command not including python source files.
+
 # 0.6.8
 
     - Update CD commands for newer build system.

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,5 +1,5 @@
 include *.txt
 include *.md
-include ripser/pyRips.pxd
-include ripser/ripser.cpp
-include ripser/pyRipser.pyx
+include src/ripser/pyRips.pxd
+include src/ripser/ripser.cpp
+include src/ripser/pyRipser.pyx
diff --git a/README.md b/README.md
@@ -29,7 +29,15 @@ If you're looking for a GPU-accelerated version of Ripser, you can find it at [R
 
 ## Setup
 
-Ripser.py is available on all major platforms. All that is required is that you install the standard Python numerical computing libraries and Cython.
+Ripser.py is available on `pypi` with wheels for all major platforms. To install, type the following command into your environment:
+
+```bash
+pip install python
+```
+### Local build
+
+If the above command fails, you can build `ripser.py` locally. All that is required is that you 
+install the standard Python numerical computing libraries and Cython.
 
 Dependencies:
 
@@ -47,33 +55,35 @@ Cython should be the only library required before installation. To install, type
 
 ```
 pip install cython
-pip install ripser
 ```
 
-If you are having trouble installing, please let us know!
+Following this, clone the repository, `cd` into the clone, and execute `pip install -v .`
 
-## Optional dependency
+
+#### Optional dependency
 
 Ripser.py when compiled from source can have a _steroid_<sup>1</sup> shot by replacing the standard `unordered_map` from the STL by one of the fastest implementation available: [robin_hood](https://github.com/martinus/robin-hood-hashing). Benchmarking of Ripser.py using the `robin_hood` implementation showed speed-ups up to **30%**.
 
 To be able to use `robin_hood` instead of STL, you only need to clone the repository containing the implementation:
 
 ```
 # Run this command at the root of the project
-git clone https://github.com/martinus/robin-hood-hashing ripser/robinhood
+git clone https://github.com/martinus/robin-hood-hashing robinhood
 ```
 
 After cloning robinhood with the above command, install `ripser.py` with
 
 ```
-pip install -v -e .
+pip install -v .
 ```
 
-This will install a local, editable version of `ripser.py` with verbose output. In the verbose output,
+This will install a local version of `ripser.py` with verbose output. In the verbose output,
 you will see confirmation that robinhood was found or not.
 
 <sup>1</sup> The Python package is already compiled with `robin_hood` by default.
 
+If you are having trouble installing, please let us know!
+
 ## Usage
 
 The interface is as simple as can be:

diff --git a/pyproject.toml b/pyproject.toml
@@ -47,9 +47,6 @@ docs = ["sktda_docs_config"]
 
 examples = ["tadasets", "jupyter", "pillow"]
 
-[tool.setuptools.packages.find]
-where = ["ripser"]
-
 [project.urls]
 Homepage = "https://ripser.scikit-tda.org"
 Documentation = "https://ripser.scikit-tda.org"

diff --git a/ripser/_version.py b/ripser/_version.py
diff --git a/setup.py b/setup.py
@@ -16,7 +16,7 @@
 
 
 def get_version():
-    VERSIONFILE = "ripser/_version.py"
+    VERSIONFILE = "src/ripser/_version.py"
     verstrline = open(VERSIONFILE, "rt").read()
     VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
     mo = re.search(VSRE, verstrline, re.M)
@@ -60,7 +60,7 @@ def run(self):
 macros = [("USE_COEFFICIENTS", 1), ("NDEBUG", 1), ("ASSEMBLE_REDUCTION_MATRIX", 1)]
 
 # Robinhood
-robinhood_path = os.path.join("ripser", "robinhood")
+robinhood_path = os.path.join("robinhood")
 if os.path.isdir(robinhood_path):
     print(
         "\nFound local copy of robinhood! Using robinhood for ripser.py compilation.\n"
@@ -81,7 +81,7 @@ def run(self):
 
 ext_modules = Extension(
     "pyRipser",
-    sources=["ripser/pyRipser.pyx"],
+    sources=["src/ripser/pyRipser.pyx"],
     define_macros=macros,
     extra_compile_args=extra_compile_args,
     extra_link_args=extra_link_args,

diff --git a/ripser/__init__.py → src/ripser/__init__.py b/ripser/__init__.py → src/ripser/__init__.py
diff --git a/src/ripser/_version.py b/src/ripser/_version.py
@@ -0,0 +1 @@
+__version__ = "0.6.10"
diff --git a/ripser/pyRips.pxd → src/ripser/pyRips.pxd b/ripser/pyRips.pxd → src/ripser/pyRips.pxd
diff --git a/ripser/pyRipser.pyx → src/ripser/pyRipser.pyx b/ripser/pyRipser.pyx → src/ripser/pyRipser.pyx
diff --git a/ripser/ripser.cpp → src/ripser/ripser.cpp b/ripser/ripser.cpp → src/ripser/ripser.cpp
diff --git a/ripser/ripser.h → src/ripser/ripser.h b/ripser/ripser.h → src/ripser/ripser.h
diff --git a/ripser/ripser.py → src/ripser/ripser.py b/ripser/ripser.py → src/ripser/ripser.py