diffstar 0.2.0__tar.gz → 0.2.2__tar.gz

diffstar-0.2.0/.github/workflows/tests.yml → diffstar-0.2.2/.github/workflows/linting.yml

@@ -1,4 +1,4 @@
-name: tests
+name: linting
 
 on:
   push:
@@ -26,25 +26,13 @@ jobs:
       - name: configure conda and install code
         shell: bash -l {0}
         run: |
-          conda config --set always_yes yes
-          conda install --quiet \
+          mamba install --quiet \
             --file=requirements.txt
           python -m pip install --no-deps -e .
-          conda install -y -q \
-            flake8 \
-            pytest \
-            pytest-xdist \
-            pytest-cov
+          mamba install -y -q \
+            flake8
 
       - name: lint
         shell: bash -l {0}
         run: |
           flake8 diffstar
-
-      - name: test
-        shell: bash -l {0}
-        run: |
-          pytest -v diffstar --cov --cov-report=xml
-
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3

diffstar-0.2.2/.github/workflows/tests.yml

@@ -0,0 +1,81 @@
+name: tests
+
+on:
+  workflow_dispatch: null
+  schedule:
+    # Runs "every Monday & Thursday at 3:05am Central"
+    - cron: '5 8 * * 1,4'
+  push:
+    branches:
+      - main
+  pull_request: null
+
+jobs:
+  tests:
+    name: tests
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.9
+          channels: conda-forge,defaults
+          channel-priority: strict
+          show-channel-urls: true
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+
+      - name: configure conda and install code
+        shell: bash -l {0}
+        run: |
+          conda config --set always_yes yes
+          mamba install --quiet \
+            --file=requirements.txt
+          python -m pip install --no-deps -e .
+          mamba install -y -q \
+            flake8 \
+            pytest \
+            pytest-xdist \
+            pytest-cov \
+            pip \
+            setuptools \
+            "setuptools_scm>=7,<8" \
+            python-build
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: test
+        shell: bash -l {0}
+        run: |
+          pytest -v diffstar --cov --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+
+      - name: test versions
+        shell: bash -el {0}
+        run: |
+          pip uninstall diffstar --yes
+          [[ $(python setup.py --version) != "0.0.0" ]] || exit 1
+
+          rm -rf dist/*
+          python setup.py sdist
+          pip install --no-deps --no-build-isolation dist/*.tar.gz
+          pushd ..
+          python -c "import diffstar; assert diffstar.__version__ != '0.0.0'"
+          popd
+          pip uninstall diffstar --yes
+
+          rm -rf dist/*
+          python -m build --sdist . --outdir dist
+          pip install --no-deps --no-build-isolation dist/*.tar.gz
+          pushd ..
+          python -c "import diffstar; assert diffstar.__version__ != '0.0.0'"
+          popd
+          pip uninstall diffstar --yes
+
+          python -m pip install -v --no-deps --no-build-isolation -e .

{diffstar-0.2.0 → diffstar-0.2.2}/CHANGES.rst

@@ -1,3 +1,13 @@
+0.2.2 (2023-10-08)
+------------------
+- Fix forgotten import so that diffstar.__version__ now works
+
+
+0.2.1 (2023-09-27)
+------------------
+- Implement floor at SFR_MIN in all computations of SFH
+
+
 0.2.0 (2023-09-25)
 ------------------
 - Remove quenching.py module

{diffstar-0.2.0 → diffstar-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffstar
-Version: 0.2.0
+Version: 0.2.2
 Summary: Differentiable Star Formation Histories
 Author-email: Alex Alarcon <alexalarcongonzalez@gmail.com>
 License: BSD 3-Clause License
@@ -47,7 +47,7 @@ Requires-Dist: h5py
 ## Installation
 The latest release of diffstar is available for installation with either pip or conda-forge:
 ```
-$ conda install diffstar
+$ conda install -c conda-forge diffstar
 ```
 
 Alternatively, to install diffstar into your environment from the source code:
@@ -58,10 +58,10 @@ $ pip install .
 ```
 
 ### Environment configuration
-For a typical development environment in conda:
+For a typical development environment with conda-forge:
 
 ```
-$ conda create -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
+$ conda create -c conda-forge -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
 ```
 
 ## Project data

{diffstar-0.2.0 → diffstar-0.2.2}/README.md

@@ -3,7 +3,7 @@
 ## Installation
 The latest release of diffstar is available for installation with either pip or conda-forge:
 ```
-$ conda install diffstar
+$ conda install -c conda-forge diffstar
 ```
 
 Alternatively, to install diffstar into your environment from the source code:
@@ -14,10 +14,10 @@ $ pip install .
 ```
 
 ### Environment configuration
-For a typical development environment in conda:
+For a typical development environment with conda-forge:
 
 ```
-$ conda create -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
+$ conda create -c conda-forge -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
 ```
 
 ## Project data

{diffstar-0.2.0 → diffstar-0.2.2}/diffstar/__init__.py

@@ -1,7 +1,6 @@
 """
 """
 # flake8: noqa
-
-
+from ._version import __version__
 from .kernels import get_ms_sfh_from_mah_kern, get_sfh_from_mah_kern
 from .sfh import sfh_galpop, sfh_singlegal

diffstar-0.2.2/diffstar/_version.py

@@ -0,0 +1 @@
+__version__ = '0.2.2'

{diffstar-0.2.0 → diffstar-0.2.2}/diffstar/kernels/kernel_builders.py

@@ -5,7 +5,7 @@ from jax import lax
 from jax import numpy as jnp
 from jax import vmap
 
-from ..defaults import DEFAULT_N_STEPS, T_BIRTH_MIN
+from ..defaults import DEFAULT_N_STEPS, SFR_MIN, T_BIRTH_MIN
 from .main_sequence_kernels import _get_bounded_sfr_params, _lax_ms_sfh_scalar_kern
 from .quenching_kernels import _quenching_kern_u_params
 
@@ -64,6 +64,7 @@ def get_sfh_from_mah_kern(
         lgt_form = jnp.log10(t_form)
         qfunc = _quenching_kern_u_params(lgt_form, *u_q_params)
         sfr = qfunc * ms_sfr
+        sfr = lax.cond(sfr < SFR_MIN, lambda x: SFR_MIN, lambda x: x, sfr)
         return sfr
 
     kern_with_tobs_loop = _get_kern_with_tobs_loop(_kern, tobs_loop)
@@ -167,7 +168,9 @@ def get_ms_sfh_from_mah_kern(
         t_min = jnp.max(jnp.array((tacc_integration_min, t_form - tau_dep)))
         t_table = t_min + uniform_table * (t_form - t_min)
         args = t_form, mah_params, ms_params, lgt0, fb, t_table
-        return _lax_ms_sfh_scalar_kern(*args)
+        sfr = _lax_ms_sfh_scalar_kern(*args)
+        sfr = lax.cond(sfr < SFR_MIN, lambda x: SFR_MIN, lambda x: x, sfr)
+        return sfr
 
     kern_with_tobs_loop = _get_ms_kern_with_tobs_loop(_kern, tobs_loop)
     lax_ms_sfh_from_mah_kern = _get_ms_kern_with_galpop_loop(

{diffstar-0.2.0 → diffstar-0.2.2}/diffstar/tests/test_sfh.py

@@ -172,3 +172,27 @@ def test_fb_value_propagates_to_sfh_galpop():
     x = 2.0
     sfh2 = sfh_galpop(tarr, mah_params, ms_params, q_params, LGT0, FB * x)
     assert np.allclose(sfh2, x * sfh)
+
+
+def test_sfh_galpop_is_always_strictly_positive():
+    n_gals, n_t = 1_000, 100
+    lgt0, mah_params, __, __ = _get_all_default_params()
+    tarr = np.linspace(0.1, 10**lgt0, n_t)
+
+    mah_params_singlegal = np.array((12.0, 0.0, 3.0, 2.0))
+    mah_params_galpop = np.tile(mah_params_singlegal, n_gals).reshape((n_gals, 4))
+    u_ms_params_galpop = np.random.uniform(-100, 100, size=(n_gals, 5))
+    u_q_params_galpop = np.random.uniform(-100, 100, size=(n_gals, 4))
+
+    sfh = sfh_galpop(
+        tarr,
+        mah_params_galpop,
+        u_ms_params_galpop,
+        u_q_params_galpop,
+        LGT0,
+        FB,
+        ms_param_type="unbounded",
+        q_param_type="unbounded",
+    )
+    assert np.all(np.isfinite(sfh))
+    assert np.all(sfh >= SFR_MIN)

{diffstar-0.2.0 → diffstar-0.2.2}/diffstar.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffstar
-Version: 0.2.0
+Version: 0.2.2
 Summary: Differentiable Star Formation Histories
 Author-email: Alex Alarcon <alexalarcongonzalez@gmail.com>
 License: BSD 3-Clause License
@@ -47,7 +47,7 @@ Requires-Dist: h5py
 ## Installation
 The latest release of diffstar is available for installation with either pip or conda-forge:
 ```
-$ conda install diffstar
+$ conda install -c conda-forge diffstar
 ```
 
 Alternatively, to install diffstar into your environment from the source code:
@@ -58,10 +58,10 @@ $ pip install .
 ```
 
 ### Environment configuration
-For a typical development environment in conda:
+For a typical development environment with conda-forge:
 
 ```
-$ conda create -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
+$ conda create -c conda-forge -n diffit python=3.9 numpy numba flake8 pytest jax ipython jupyter matplotlib scipy h5py diffmah diffstar
 ```
 
 ## Project data

{diffstar-0.2.0 → diffstar-0.2.2}/diffstar.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ pyproject.toml
 requirements.txt
 setup.cfg
 setup.py
+.github/workflows/linting.yml
 .github/workflows/tests.yml
 diffstar/__init__.py
 diffstar/_version.py

diffstar-0.2.0/diffstar/_version.py

@@ -1 +0,0 @@
-__version__ = '0.2.0'