Merge branch 'main' into paper

.gitignore

@@ -55,3 +55,5 @@ MANIFEST
 src/xtal2png/meta.yaml
 xtal2png/meta.yaml
 tmp/**
+results/model-*.pt
+results/sample-*.png

CHANGELOG.md

@@ -1,5 +1,36 @@
 # CHANGELOG
 
+## Unreleased
+
+Changes unreleased.
+
+### Bug Fixes
+
+- general:
+  - fix typos, remove extraneous figure, add future work ([d0ffb91](https://github.com/sparks-baird/xtal2png/commit/d0ffb917e062c0a580a42dc5ee5309c4e036e48f)) ([#67](https://github.com/sparks-baird/xtal2png/pull/67))
+
+## [v0.4.0](https://github.com/sparks-baird/xtal2png/releases/tag/v0.4.0) - 2022-06-03 02:01:29
+
+<!-- Release notes generated using configuration in .github/release.yml at v0.4.0 -->
+
+## What's Changed
+### Other Changes
+* available on conda-forge by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/49
+* fix colab link in index.md by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/53
+* add colab link to README by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/52
+* fixup colab link by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/56
+* add note about needing development versions of pyscaffold and extensions by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/58
+* Support rgb images in `png2xtal` by converting to grayscale by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/62
+
+
+**Full Changelog**: https://github.com/sparks-baird/xtal2png/compare/v0.3.0...v0.4.0
+
+### Bug Fixes
+
+- general:
+  - fixup colab link ([7803383](https://github.com/sparks-baird/xtal2png/commit/7803383b2e1acbb565b417d82606a6c40ac425b8)) ([#56](https://github.com/sparks-baird/xtal2png/pull/56))
+  - fix colab link in index.md ([7ff9bfa](https://github.com/sparks-baird/xtal2png/commit/7ff9bface93181f40fcf9e733dd082f737249b74)) ([#53](https://github.com/sparks-baird/xtal2png/pull/53))
+
 ## [v0.3.0](https://github.com/sparks-baird/xtal2png/releases/tag/v0.3.0) - 2022-05-31 17:28:49
 
 <!-- Release notes generated using configuration in .github/release.yml at v0.3.0  -->
@@ -61,10 +92,7 @@ Feature ranges for `a`, `b`, `c`, `volume`, and `distance` are chosen based on M
 
 ## [v0.1.6](https://github.com/sparks-baird/xtal2png/releases/tag/v0.1.6) - 2022-05-27 05:36:46
 
-- no changes
-
 <!-- Release notes generated using configuration in .github/release.yml at v0.1.6 -->
-
 ## What's Changed
 ### Other Changes
 * minor typos, clarification by @sgbaird in https://github.com/sparks-baird/xtal2png/pull/29

notebooks/3.0-denoising-diffusion.ipynb

@@ -0,0 +1,19 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

notebooks/ddpm.py

@@ -0,0 +1,49 @@
+from os import path
+
+from denoising_diffusion_pytorch import GaussianDiffusion, Trainer, Unet
+from mp_time_split.core import MPTimeSplit
+
+from xtal2png.core import XtalConverter
+
+mpt = MPTimeSplit()
+mpt.load()
+
+fold = 0
+train_inputs, val_inputs, train_outputs, val_outputs = mpt.get_train_and_val_data(fold)
+
+data_path = path.join("data", "preprocessed", "mp-time-split")
+xc = XtalConverter(save_dir=data_path)
+
+model = Unet(dim=64, dim_mults=(1, 2, 4, 8), channels=1).cuda()
+
+diffusion = GaussianDiffusion(
+    model,
+    channels=1,
+    image_size=64,
+    timesteps=10000,  # number of steps
+    loss_type="l1",  # L1 or L2
+).cuda()
+
+trainer = Trainer(
+    diffusion,
+    data_path,
+    image_size=64,
+    train_batch_size=2,
+    train_lr=2e-5,
+    train_num_steps=700000,  # total training steps
+    gradient_accumulate_every=2,  # gradient accumulation steps
+    ema_decay=0.995,  # exponential moving average decay
+    amp=True,  # turn on mixed precision
+)
+
+trainer.train()
+
+sampled_images = diffusion.sample(batch_size=100)
+
+# import numpy as np
+# from PIL import Image
+# data = np.squeeze(sampled_images.cpu().numpy())
+# imgs = []
+# for d in data:
+#     img = Image.fromarray(d, mode="L")
+#     imgs.append(img)

reports/paper.md

@@ -15,7 +15,7 @@ authors:
     orcid: 0000-0002-6583-7755
     equal-contrib: false
     affiliation: "1" # (Multiple affiliations must be quoted)
-  - name: Michael Alverson
+  - name: Michael D. Alverson
     orcid: 0000-0002-4857-7584
     equal-contrib: false
     affiliation: "1, 2" # (Multiple affiliations must be quoted)

scripts/run_grayskull.py

@@ -1,12 +1,13 @@
 """Touch up the conda recipe from grayskull using conda-souschef."""
 import os
-from copy import deepcopy
+from copy import copy
 from os import getcwd
 from os.path import basename, dirname, join, normpath
 from pathlib import Path
 from shutil import copyfile
 from warnings import warn
 
+import numpy as np
 from souschef.recipe import Recipe
 
 import xtal2png as module
@@ -16,6 +17,11 @@
 
 name, version = module.__name__, module.__version__
 
+replace_underscores_with_hyphens = True
+
+if replace_underscores_with_hyphens:
+    name = name.replace("_", "-")
+
 src_dirname = "src"
 if basename(normpath(getcwd())) != src_dirname:
     warn(
@@ -45,12 +51,31 @@
 
 my_recipe = Recipe(load_file=fpath)
 
-bld = my_recipe["build"]
-bld.add_section({"noarch": "python"})
-blank_line = deepcopy(bld.value[bld.value.index("")])
-bld.value[bld.value.index("")].remove()
-# how to add blank_line back in? Following doesn't seem to work:
-bld.value = bld.value + [blank_line]
+# ensure proper order for conda-forge
+keys = list(my_recipe.keys())
+
+# https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
+key_order = [
+    "package",
+    "source",
+    "build",
+    "requirements",
+    "test",
+    "outputs",
+    "about",
+    "app",
+    "extra",
+]
+unshared_keys = np.setdiff1d(key_order, keys)
+
+ordered_keys = copy(key_order)
+for key in unshared_keys:
+    ordered_keys.remove(key)
+
+for key in ordered_keys:
+    my_recipe.yaml.move_to_end(key)
+
+my_recipe["build"].add_section({"noarch": "python"})
 
 try:
     del my_recipe["build"]["skip"]
@@ -81,7 +106,7 @@
 # my_recipe["about"].insert(0, "key", "value")
 
 # # sometimes package names differ between PyPI and Anaconda (e.g. `kaleido`)
-# my_recipe["requirements"]["run"].replace("kaleido", "python-kaleido")
+my_recipe["requirements"]["run"].replace("kaleido", "python-kaleido")
 
 # # It's better to install some packages either exclusively via Anaconda or
 # # via custom PyPI installation instructions (see e.g. the selectable table from: