Release/0.10.0

.github/actions/setup-python/action.yaml

@@ -0,0 +1,45 @@
+name: Setup Python Environment
+description: Setup Python, reinstall pip, and install dependencies
+inputs:
+  python-version:
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Cache pip dependencies
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Reinstall pip
+      shell: bash
+      run: |
+        PY_VER=$(python -c "import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')")
+        PY_MAJOR=$(echo $PY_VER | cut -d. -f1)
+        PY_MINOR=$(echo $PY_VER | cut -d. -f2)
+
+        if [ "$PY_MAJOR" -eq 3 ] && [ "$PY_MINOR" -le 8 ]; then
+          URL="https://bootstrap.pypa.io/pip/${PY_VER}/get-pip.py"
+        else
+          URL="https://bootstrap.pypa.io/get-pip.py"
+        fi
+
+        curl -sS "$URL" -o /tmp/get-pip.py
+        python /tmp/get-pip.py --force-reinstall
+
+        pip --version
+        pip3 --version
+
+    - name: Install dependencies
+      shell: bash
+      run: |
+        python3 -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install --upgrade -r requirements.txt; fi
+        pip3 install --upgrade -r requirements/dev.txt

.github/workflows/push-pr_workflow.yml

@@ -9,66 +9,60 @@ jobs:
     if: github.event_name == 'pull_request'
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # Checkout the whole history, in case the target is way far behind
+
+    - name: Check if target branch has been merged
+      run: |
+        if git merge-base --is-ancestor ${{ github.event.pull_request.base.sha }} ${{ github.sha }}; then
+          echo "Target branch has been merged into the source branch."
+        else
+          echo "Target branch has not been merged into the source branch. Please merge in target first."
+          exit 1
+        fi
 
     - name: Check that CHANGELOG has been updated
       run: |
         # If this step fails, this means you haven't updated the CHANGELOG.md file with notes on your contribution.
-        git diff --name-only $(git merge-base origin/main HEAD) | grep '^CHANGELOG.md$' && echo "Thanks for helping keep our CHANGELOG up-to-date!"
+        if git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep -q '^CHANGELOG.md$'; then
+          echo "Thanks for helping keep our CHANGELOG up-to-date!"
+        else
+          echo "Please update the CHANGELOG.md file with notes on your contribution."
+          exit 1
+        fi
 
   Lint:
     runs-on: ubuntu-latest
     env:
-      MAX_LINE_LENGTH: 88
-      MAX_COMPLEXITY: 18
+      MAX_LINE_LENGTH: 127
+      MAX_COMPLEXITY: 15
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
+    - uses: actions/checkout@v4
 
-    - name: Check cache
-      uses: actions/cache@v2
+    - uses: ./.github/actions/setup-python
       with:
-        path: ~/.cache/pip
-        key: ${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
-
-    - name: Install dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install --upgrade -r requirements.txt; fi
-        pip3 install --upgrade -r requirements/dev.txt
+        python-version: '3.x'    
 
     - name: Lint with flake8
-      if: always()
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --max-complexity=$MAX_COMPLEXITY --statistics --max-line-length=$MAX_LINE_LENGTH
 
     - name: Lint with isort
-      if: always()
       run: |
-        python3 -m isort --check --line-length $MAX_LINE_LENGTH spellbook
-        # Skipping test_conduit due to temporary fix for missing conduit python package.
-        python3 -m isort --check --line-length $MAX_LINE_LENGTH --skip tests/data_formatting/conduit/test_conduit.py tests
-        python3 -m isort --check --line-length $MAX_LINE_LENGTH *.py
+        isort --check --line-length $MAX_LINE_LENGTH spellbook tests *.py
 
     - name: Lint with Black
-      if: always()
       run: |
-        python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py36 spellbook
-        python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py36 tests
-        python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py36 *.py
+        black --check --line-length $MAX_LINE_LENGTH --target-version py311 spellbook tests *.py
 
     - name: Lint with PyLint
-      if: always()
       run: |
-        python3 -m pylint spellbook --rcfile=setup.cfg --exit-zero
-        python3 -m pylint tests --rcfile=setup.cfg --exit-zero
+        pylint spellbook tests --rcfile=setup.cfg --exit-zero
 
   Local-test-suite:
     runs-on: ubuntu-latest
@@ -78,23 +72,11 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
+    - uses: actions/checkout@v4
 
-    - name: Check cache
-      uses: actions/cache@v2
+    - uses: ./.github/actions/setup-python
       with:
-        path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
-
-    - name: Install dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        pip3 install -r requirements/dev.txt
+        python-version: ${{ matrix.python-version }}
 
     - name: Install merlin-spellbook to run unit tests
       run: |

CHANGELOG.md

@@ -4,6 +4,23 @@ All notable changes to Merlin Spellbook will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.0]
+
+### Added
+- Added normal and truncnorm distributions
+- COPYRIGHT file for ownership details
+- New check for copyright headers in the Makefile
+
+### Changed
+- Updated GitHub actions
+    - Now uses a version of actions/cache that's not deprecated
+    - Utilizes a shared action for jobs to reduce duplicate code
+- Copyright headers in all files
+  - These now point to the LICENSE and COPYRIGHT files
+  - LICENSE: Legal permissions (e.g., MIT terms)
+  - COPYRIGHT: Ownership, institutional metadata
+  - Make commands that change version/copyright year have been modified
+
 ## [0.9.0]
 
 ### Added

CONTRIBUTORS

@@ -0,0 +1,9 @@
+Luc Peterson <[email protected]>
+Peter Robinson <[email protected]>
+Jessica Semler <[email protected]>
+Benjamin Bay
+Joe Koning <[email protected]>
+Jeremy White <[email protected]>
+Aidan Keogh
+Ryan Lee <[email protected]>
+Brian Gunnarson <[email protected]>

COPYRIGHT

@@ -0,0 +1,10 @@
+Copyright (c) 2019–2025 Lawrence Livermore National Laboratory
+
+Produced at the Lawrence Livermore National Laboratory
+
+LLNL-CODE-797170
+
+All rights reserved.
+
+See the CONTRIBUTORS file for a full list of authors and contributors.
+See the LICENSE file for license details.

LICENSE

@@ -1,6 +1,8 @@
 MIT License
 
-Copyright (c) 2022 Lawrence Livermore National Laboratory
+See the COPYRIGHT file for ownership and authorship information.
+
+For details, see https://github.com/LLNL/merlin-spellbook.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -3,6 +3,7 @@ VER?=1.0.0
 VSTRING=[0-9]\+\.[0-9]\+\.[0-9]\+
 PYTHON?=python3
 PY_TARGET_VER?=py311  # At the time this is added (2/19/25) black only supports up to py311
+FROM?=Unreleased
 
 PROJ=spellbook
 TEST=tests
@@ -25,17 +26,22 @@ tests: unit-tests command-line-tests
 release:
 	python3 -m build .
 
-# Use like this: make VER=?.?.? verison
+# Increment the Spellbook version. USE ONLY ON DEVELOP BEFORE MERGING TO MASTER.
+# Usage: make version VER=1.13.0 FROM=1.13.0-beta
+#        (defaults to FROM=Unreleased if not set)
 version:
-	# do spellbook/__init__.py
-	sed -i 's/__version__ = "$(VSTRING)"/__version__ = "$(VER)"/g' $(PROJ)/__init__.py
-	# do CHANGELOG.md
-	sed -i 's/## \[Unreleased\]/## [$(VER)]/g' CHANGELOG.md
-	# do all file headers (works on linux)
-	find $(PROJ)/ -type f -print0 | xargs -0 sed -i 's/Version: $(VSTRING)/Version: $(VER)/g'
-	find *.py -type f -print0 | xargs -0 sed -i 's/Version: $(VSTRING)/Version: $(VER)/g'
-	find $(TEST)/ -type f -print0 | xargs -0 sed -i 's/Version: $(VSTRING)/Version: $(VER)/g'
-	find Makefile -type f -print0 | xargs -0 sed -i 's/Version: $(VSTRING)/Version: $(VER)/g'
+	@echo "Updating Spellbook version from [$(FROM)] to [$(VER)]..."
+	sed -i 's/__version__ = "\(.*\)"/__version__ = "$(VER)"/' spellbook/__init__.py
+	@if grep -q "## \[$(FROM)\]" CHANGELOG.md; then \
+		sed -i 's/## \[$(FROM)\]/## [$(VER)]/' CHANGELOG.md; \
+	else \
+		echo "⚠️  No matching '## [$(FROM)]' found in CHANGELOG.md"; \
+	fi
+
+# Increment copyright year = Usage: make year YEAR=2026
+year:
+	@echo "Updating COPYRIGHT file to year $(YEAR)..."
+	sed -i -E 's/(Copyright \(c\) 2019–)[0-9]{4}( Lawrence Livermore National Laboratory)/\1$(YEAR)\2/' COPYRIGHT
 
 clean:
 	-find $(PROJ) -name "*.py[cod]" -exec rm -f {} \;
@@ -79,4 +85,18 @@ check-pylint:
 	$(PYTHON) -m pylint $(TEST) --rcfile=setup.cfg; \
 
 
-check-style: check-flake8 check-black check-isort check-pylint
+check-copyright:
+	@echo "🔍 Checking for required copyright header..."
+	@missing_files=$$(find $(PROJ) $(TEST) \
+		-name '*.py' -print | \
+		xargs grep -L "Copyright (c) Lawrence Livermore National Security, LLC and other" || true); \
+	if [ -n "$$missing_files" ]; then \
+		echo "❌ The following files are missing the required copyright header:"; \
+		echo "$$missing_files"; \
+		exit 1; \
+	else \
+		echo "✅ All files contain the required header."; \
+	fi
+
+
+check-style: check-copyright check-flake8 check-black check-isort check-pylint

setup.cfg

@@ -3,16 +3,16 @@ multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0
 use_parentheses=True
-line_length=88
+line_length=127
 known_first_party=merlin
 known_third_party=psutil,conduit,matplotlib,pandas,numpy
 lines_after_imports=2
 
 
 [flake8]
 ignore = E203, E266, E501, W503
-max-line-length = 88
-max-complexity = 18
+max-line-length = 127
+max-complexity = 15
 select = B,C,E,F,W,T4
 
 [mypy]

setup.py

@@ -1,32 +1,10 @@
-###############################################################################
-# Copyright (c) 2022, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory
-# Written by the Merlin dev team, listed in the CONTRIBUTORS file.
-# <[email protected]>
-#
-# LLNL-CODE-797170
-# All rights reserved.
-# This file is part of Merlin-Spellbook, Version: 0.9.0.
-#
-# For details, see https://github.com/LLNL/merlin-spellbook.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-###############################################################################
+##############################################################################
+# Copyright (c) Lawrence Livermore National Security, LLC and other
+# Merlin-Spellbook Project developers. See top-level LICENSE and COPYRIGHT
+# files for dates and other details. No copyright assignment is required to
+# contribute to Merlin-Spellbook.
+##############################################################################
+
 
 import os
 
@@ -58,10 +36,7 @@ def _pip_requirement(req):
 def _reqs(*f):
     return [
         _pip_requirement(r)
-        for r in (
-            _strip_comments(line)
-            for line in open(os.path.join(os.getcwd(), "requirements", *f)).readlines()
-        )
+        for r in (_strip_comments(line) for line in open(os.path.join(os.getcwd(), "requirements", *f)).readlines())
         if r
     ]
 

spellbook/__init__.py

@@ -1,3 +1,10 @@
-__version__ = "0.9.0"
+##############################################################################
+# Copyright (c) Lawrence Livermore National Security, LLC and other
+# Merlin-Spellbook Project developers. See top-level LICENSE and COPYRIGHT
+# files for dates and other details. No copyright assignment is required to
+# contribute to Merlin-Spellbook.
+##############################################################################
+
+__version__ = "0.10.0"
 
 VERSION = __version__

spellbook/__main__.py

@@ -1,3 +1,10 @@
+##############################################################################
+# Copyright (c) Lawrence Livermore National Security, LLC and other
+# Merlin-Spellbook Project developers. See top-level LICENSE and COPYRIGHT
+# files for dates and other details. No copyright assignment is required to
+# contribute to Merlin-Spellbook.
+##############################################################################
+
 import sys
 
 from spellbook.main import main

spellbook/commands/__init__.py

@@ -1,3 +1,10 @@
+##############################################################################
+# Copyright (c) Lawrence Livermore National Security, LLC and other
+# Merlin-Spellbook Project developers. See top-level LICENSE and COPYRIGHT
+# files for dates and other details. No copyright assignment is required to
+# contribute to Merlin-Spellbook.
+##############################################################################
+
 from abc import ABC, abstractmethod