Merge pull request #42 from tberlok/presubmit

Presubmit

.github/workflows/manylinux.yml

@@ -44,5 +44,12 @@ jobs:
         # twine upload --repository-url https://test.pypi.org/legacy/ dist/*manylinux*
 
         # Commands for uploading to pypi
-        #twine upload dist/*tar.gz
+        twine upload dist/*tar.gz
         twine upload dist/*manylinux*
+
+        # How to make a pip installation on my Mac:
+        # make clean
+        # python3 setup.py sdist bdist_wheel
+        # twine check dist/*
+        # twine upload dist/*
+

.github/workflows/pylint.yml

@@ -41,4 +41,4 @@ jobs:
         run: make
 
       - name: Validate
-        run: pylint --errors-only --ignored-modules=astropy.units,astropy.constants  --disable=E0611,E0401,E1101,E1120,E1121 paicos
+        run: pylint --errors-only --ignored-modules=astropy.units,astropy.constants  --disable=E0611,E0401,E1101,E1120,E1121,E1111 paicos

MANIFEST.in

@@ -0,0 +1,2 @@
+global-include *.pyx
+global-exclude *.c

Makefile

@@ -12,26 +12,26 @@ clean:
 	rm -rf paicos.egg-info
 
 cleanup:
-	rm -rf test_data
+	rm -rf data/test_data
 	rm -f data/very_small_snap_247.hdf5
 	rm -f data/reduced_snap2_247.hdf5
 
 checks:
 	make cleanup
-	pytest tests/comoving
-	pytest tests/non-comoving
-	pytest tests/general
+	cd tests; pytest comoving
+	cd tests; pytest non-comoving
+	cd tests; pytest general
 
 linting:
 	flake8 ./
-	pylint --errors-only --ignored-modules=astropy.units,astropy.constants  --disable=E0611,E0401,E1101,E1120,E1121 paicos
+	pylint --errors-only --ignored-modules=astropy.units,astropy.constants  --disable=E0611,E0401,E1101,E1120,E1121,E1111 paicos
 
-make dev_checks:
+dev_checks:
 	make checks
 	make linting
 
 # Tests that can only run on some systems
-make gpu_checks:
-	python tests/cuda-gpu/test_gpu_binary_tree.py
-	python tests/cuda-gpu/test_gpu_ray_projector.py
-	python tests/cuda-gpu/test_gpu_sph_projector.py
+gpu_checks:
+	cd tests; python cuda-gpu/test_gpu_binary_tree.py
+	cd tests; python cuda-gpu/test_gpu_ray_projector.py
+	cd tests; python cuda-gpu/test_gpu_sph_projector.py

docs/source/conf.py

@@ -26,7 +26,7 @@
 project = 'Paicos'
 copyright = '2023, Thomas Berlok'
 author = 'Thomas Berlok'
-release = '0.1.6'
+release = '0.1.8'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/examples.md

@@ -1,7 +1,7 @@
 # Running the examples and notebooks
 
 We provide a number of examples in the subdirectories `examples/` and `ipython-notebooks`.
-We recommend that you start by working your way through the notebooks, startting with
+We recommend that you start by working your way through the notebooks, starting with
 notebook 1a.
 
 ## Downloading sample data

docs/source/installation.md

@@ -30,15 +30,17 @@ in my `.bash_profile`.
 #### Compiling on MacOs
 
 You will need an openmp-enabled compiler. On MacOs, you can install gcc via homebrew.
-The `setup.py` in the Paicos directory currently has the following hardcoded
-compiler option. 
+You can then either modify `setup.py` with your
+compiler option, .e.g.,
 ```
 if sys.platform == 'darwin':
     os.environ['CC'] = 'gcc-13'
     os.environ['CXX'] = 'g++-13'
 ```
+or by running `CC=gcc-13 make` instead of simply `make`.
+
 If you have installed gcc via homebrew, then you can get your compiler version by running
-`brew info gcc` and update `setup.py` accordingly if that does not agree with what is hardcoded.
+`brew info gcc`, which you can use to modify the instructions above accordingly.
 
 
 #### Compiling Paicos inside a notebook
@@ -52,7 +54,28 @@ make clean
 make
 ```
 
-## Option 2: Installing the development version using pip 
+## Option 2: Installing directly via pip
+
+This is probably the simplest way of installing Paicos, i.e. you run
+```
+pip install paicos
+```
+in a terminal.
+
+Note however, that this installation does not include the tests, examples
+and example data.
+
+On MacOs you might have to do something like (see details above)
+```
+CC=gcc-13 pip install paicos
+```
+If the installation succeeded then you can proceed:
+```
+# Check if installation worked and that you can import Paicos 
+python -c "import paicos"
+```
+
+## Option 3: Installing the development version using pip 
 ```
 git clone git@github.com:tberlok/paicos.git
 cd paicos
@@ -61,14 +84,39 @@ python3 -m pip install -e .
 make checks
 ```
 
-## Option 3: Installing directly via pip
+## GPU/CUDA requirements
+
+The visualization routines that run on GPU require installing CuPy (a drop-in replacement
+for NumPy that runs on the GPU) and Numba CUDA (just-in-time compilation of kernel
+and device functions on the GPU). These packages only work on CUDA-enabled GPUs,
+which means that you need a recent Nvidia GPU.
+
+These packages (CuPy and Numba) are not automatically included in Paicos.
+Up-to-date instructions for installing them can be found at:
+
+- CuPy: https://docs.cupy.dev/en/stable/install.html
+
+- Numba: https://numba.readthedocs.io/en/stable/cuda/overview.html#supported-gpus
+
+At the time of writing, we have had success installing for CUDA version
+11.2 using
 
-This installation does not include the tests and examples and will probably mostly work on Linux machines
 ```
-pip install paicos
+pip install numba
+pip install cupy-cuda112
+```
+and then setting the path to the CUDA installation in .bashrc as e.g.
+(substitute with the path to the CUDA installation on your system)
+```
+export CUDA_HOME=/software/astro/cuda/11.2 # numba
+export CUDA_PATH=/software/astro/cuda/11.2 # cupy
 ```
 
+Finally, you need to add
 ```
-# Check if installation worked and that you can import Paicos 
-python -c "import paicos"
+# Whether to load GPU/cuda functionality on startup
+pa.load_cuda_functionality_on_startup(True)
 ```
+to your `user_settings.py`.
+
+

docs/source/notebooks/creating_radial_profiles.ipynb

@@ -31,7 +31,7 @@
     "import numpy as np\n",
     "\n",
     "# Open an Arepo snapshot\n",
-    "snap = pa.Snapshot(pa.root_dir + \"/data\", 247)\n",
+    "snap = pa.Snapshot(pa.data_dir, 247)\n",
     "\n",
     "# The center of the most massive Friends-of-friends group in the simulation\n",
     "center = snap.Cat.Group[\"GroupPos\"][0]\n",
@@ -86,7 +86,7 @@
    ],
    "source": [
     "# Create a Paicos writer object\n",
-    "radfile = pa.PaicosWriter(snap, pa.root_dir + 'data', basename='radial')\n",
+    "radfile = pa.PaicosWriter(snap, pa.data_dir, basename='radial')\n",
     "\n",
     "# Set up the binning\n",
     "bins = [1e-2*r_max, r_max, 100]\n",
@@ -168,7 +168,7 @@
     "for parttype in range(1, snap.nspecies):\n",
     "    pstr = '{}_'.format(parttype)\n",
     "    # Re-open the Arepo snapshot\n",
-    "    snap = pa.Snapshot(pa.root_dir + \"/data\", 247)\n",
+    "    snap = pa.Snapshot(pa.data_dir, 247)\n",
     "\n",
     "    # Use OpenMP parallel Cython code to find this central sphere\n",
     "    index = pa.util.get_index_of_radial_range(snap[pstr+'Coordinates'],\n",

docs/source/notebooks/histogram2d.ipynb

@@ -31,7 +31,7 @@
     "import numpy as np\n",
     "\n",
     "# A snapshot object\n",
-    "snap = pa.Snapshot(pa.root_dir + 'data', 247, load_catalog=False)\n",
+    "snap = pa.Snapshot(pa.data_dir, 247, load_catalog=False)\n",
     "\n",
     "# Create histogram\n",
     "rhoB = pa.Histogram2D(snap, '0_Density', '0_MagneticFieldStrength', weights='0_Masses', bins_x=200,\n",
@@ -104,7 +104,7 @@
        "\n",
        "    logscale (bool): Indicates whether to use logscale for the\n",
        "                     histogram, default is True.\n",
-       "\u001b[0;31mFile:\u001b[0m           ~/projects/paicos/paicos/histograms/histogram2D.py\n",
+       "\u001b[0;31mFile:\u001b[0m           /opt/homebrew/Caskroom/miniforge/base/envs/paicos/lib/python3.10/site-packages/paicos/histograms/histogram2D.py\n",
        "\u001b[0;31mType:\u001b[0m           type\n",
        "\u001b[0;31mSubclasses:\u001b[0m     "
       ]
@@ -260,7 +260,7 @@
    "outputs": [],
    "source": [
     "# Save the histogram\n",
-    "hist.save(basedir=pa.root_dir + '/data', basename='rhoT_hist')"
+    "hist.save(basedir=pa.data_dir, basename='rhoT_hist')"
    ]
   }
  ],

docs/source/notebooks/histogram2d_plotting.ipynb

@@ -12,20 +12,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "073265ea-63a9-4033-8a5f-69c45a21abe6",
    "metadata": {},
    "outputs": [],
    "source": [
     "import paicos as pa\n",
     "\n",
     "# Load the histogram\n",
-    "rhoT = pa.Histogram2DReader(pa.root_dir + '/data', 247, basename='rhoT_hist')"
+    "rhoT = pa.Histogram2DReader(pa.data_dir, 247, basename='rhoT_hist')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "8643b210-7450-4d16-86f8-5de72ef66432",
    "metadata": {},
    "outputs": [