add cli

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -17,5 +17,23 @@ jobs:
       project: diffpy.cmi
       c_extension: false
       headless: false
+      run: |
+        set -Eeuo pipefail
+        echo "Test cmds"
+        cmi -h
+        cmi env
+        cmi pack list
+        cmi profile list
+        cmi install plotting
+        if [ "${RUNNER_OS}" != "Windows" ]; then
+          conda list | grep -i ipympl
+        else
+          source "$(cygpath -u "$CONDA")/etc/profile.d/conda.sh"
+          conda activate test
+          conda list | grep -i ipympl
+        fi
+
+        echo "Running tests for diffpy.cmi dependencies"
+        cmi install _tests
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tests-on-pr.yml

@@ -11,5 +11,23 @@ jobs:
       project: diffpy.cmi
       c_extension: false
       headless: false
+      run: |
+        set -Eeuo pipefail
+        echo "Test cmds"
+        cmi -h
+        cmi env
+        cmi pack list
+        cmi profile list
+        cmi install plotting
+        if [ "${RUNNER_OS}" != "Windows" ]; then
+          conda list | grep -i ipympl
+        else
+          source "$(cygpath -u "$CONDA")/etc/profile.d/conda.sh"
+          conda activate test
+          conda list | grep -i ipympl
+        fi
+
+        echo "Running tests for diffpy.cmi dependencies"
+        cmi install _tests
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

CHANGELOG.rst

@@ -15,4 +15,3 @@ Release notes
 * Add long description to README.
 * Add light-weight documentation migrated from old diffpy-CMI documentation.
 * Add bulk Ni PDF fitting tutorial.
-

README.rst

@@ -88,7 +88,40 @@ and run the following ::
 Getting Started
 ---------------
 
-You may consult our `online documentation <https://diffpy.github.io/diffpy.cmi>`_ for tutorials and API references.
+Use the `cmi` command-line interface to install and manage modular optional dependencies, known as `packs`,
+and to configure or execute user-defined workflows that combine multiple packs with optional post-installation steps,
+known as `profiles`. To use `cmi`, you can run the following example commands:
+
+.. code-block:: bash
+        :caption: Show available commands and options
+
+        cmi -h
+
+.. code-block:: bash
+        :caption: List installed and available packs and profiles
+
+        cmi pack list
+        cmi profile list
+
+.. code-block:: bash
+        :caption: Show details of a specific pack or profile
+
+        cmi pack show <pack_name>
+        cmi profile show <profile_name>
+
+.. code-block:: bash
+        :caption: Install a pack or profile (by name or path)
+
+        cmi install <pack_name|profile_name|/absolute/path/to/profile>
+
+.. code-block:: bash
+        :caption: List and get installed examples
+
+        cmi example list
+        cmi example (copy) <example_name>
+
+You may consult our `online documentation <https://diffpy.github.io/diffpy.cmi>`_ for more information,
+tutorials, and API references.
 
 Support and Contribute
 ----------------------

news/cmi.rst

@@ -0,0 +1,27 @@
+**Added:**
+
+* Add modules ``cli``, ``conda``, ``installer``, ``log``, ``packsmanager``, ``profilesmanager``.
+* Add cmi cli commands for managing/installing profiles and packs; example and manual commands.
+* Add `all.yml` for profile installation demonstration.
+* Add `_tests.yml` profile for profile post-steps demonstration.
+
+**Changed:**
+
+* Update names to skpkg standard.
+* Change requirements dir for packs and profiles management.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -49,11 +49,10 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-cmi = "diffpy.cmi.diffpy_cmi_app:main"
-cmi = "diffpy.cmi.diffpy_cmi_app:main"
+cmi = "diffpy.cmi.cli:main"
 
 [tool.setuptools.dynamic]
-dependencies = {file = ["requirements/pip.txt"]}
+dependencies = {file = ["requirements/packs/core.txt"]}
 
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"

requirements/conda.txt

@@ -1 +1,6 @@
-numpy
+# temporary before updating skpkg release-scripts
+packaging
+PyYAML
+diffpy.utils
+diffpy.srfit
+diffpy.structure

requirements/packs/core.txt

@@ -0,0 +1,5 @@
+packaging
+PyYAML
+diffpy.utils
+diffpy.srfit
+diffpy.structure

requirements/packs/pdf.txt

@@ -0,0 +1,2 @@
+diffpy.srreal
+pyobjcryst

requirements/packs/plotting.txt

@@ -0,0 +1,4 @@
+ipywidgets
+matplotlib
+ipympl
+py3dmol>=2.0.1

requirements/packs/scripts/_pytest.bat

@@ -0,0 +1,118 @@
+@echo off
+REM Usage:
+REM   _pytest.bat urls.txt
+REM   _pytest.bat https://host/a.tar.gz https://host/b.tgz
+REM From ChatGPT
+
+setlocal EnableExtensions EnableDelayedExpansion
+
+REM ---- temp workspace under %TEMP% ----
+set "TMPROOT=%TEMP%\remote_tests_%RANDOM%%RANDOM%"
+md "%TMPROOT%" || (echo Failed to create TMPROOT & exit /b 1)
+
+REM ---- resolve args -> URL list file ----
+if "%~2"=="" (
+  if exist "%~1" (
+    set "URLS_FILE=%~f1"
+  ) else (
+    set "URLS_FILE=%TMPROOT%\urls.txt"
+    > "%URLS_FILE%" echo %~1
+  )
+) else (
+  set "URLS_FILE=%TMPROOT%\urls.txt"
+  (for %%U in (%*) do @echo %%~U) > "%URLS_FILE%"
+)
+
+pushd "%TMPROOT%" >nul || (echo Failed to enter TMPROOT & exit /b 1)
+
+set /a i=0
+set /a overall_ec=0
+
+REM read URL file line-by-line; hand off each line to a subroutine
+for /f "usebackq delims=" %%L in ("%URLS_FILE%") do call :process_one "%%L"
+
+popd >nul
+rmdir /s /q "%TMPROOT%" >nul 2>&1
+exit /b %overall_ec%
+
+REM ===================== subroutine =====================
+:process_one
+setlocal EnableExtensions EnableDelayedExpansion
+
+REM grab the raw line and trim leading spaces
+set "url=%~1"
+if "%url%"=="" (endlocal & goto :eof)
+:trim
+if not "%url:~0,1%"==" " goto :trim_done
+set "url=%url:~1%"
+goto trim
+:trim_done
+
+REM skip comments
+if "%url:~0,1%"=="#" (endlocal & goto :eof)
+
+REM ----- do the work for this URL -----
+endlocal & set /a i+=1 & set "URL=%url%"
+echo(
+echo ==> [%i%]
+
+set "PKGDIR=%TMPROOT%\pkg_%i%"
+md "%PKGDIR%"
+pushd "%PKGDIR%" >nul || goto :after
+
+REM download archive into PKGDIR
+curl -L --fail -o "archive.tar.gz" "%URL%"
+if errorlevel 1 (
+  echo curl failed
+  set /a overall_ec=1
+  popd >nul & goto :after
+)
+
+REM extract (try gzip flags, then plain)
+tar -xzf "archive.tar.gz" >nul 2>&1
+if errorlevel 1 tar -xf "archive.tar.gz" >nul 2>&1
+if errorlevel 1 (
+  echo tar extract failed
+  set /a overall_ec=1
+  popd >nul & goto :after
+)
+
+REM get first entry (try -tzf, then -tf)
+set "FIRST="
+for /f "delims=" %%F in ('tar -tzf "archive.tar.gz" 2^>nul') do set "FIRST=%%F" & goto got_first
+for /f "delims=" %%F in ('tar -tf  "archive.tar.gz" 2^>nul') do set "FIRST=%%F" & goto got_first
+:got_first
+
+REM choose project root (top dir if present)
+set "PROJROOT=%CD%"
+if defined FIRST for /f "tokens=1 delims=/" %%T in ("%FIRST%") do if exist ".\%%T\" set "PROJROOT=%CD%\%%T"
+
+REM mirror original: drop src\ if present
+if exist "%PROJROOT%\src\" rmdir /s /q "%PROJROOT%\src" >nul 2>&1
+
+REM run pytest from repo root (with tests on PYTHONPATH if exists)
+pushd "%PROJROOT%" >nul
+echo Running pytest in: "%CD%"
+set "OLD_PYTHONPATH=%PYTHONPATH%"
+if exist "tests\" (
+  if defined OLD_PYTHONPATH (
+    set "PYTHONPATH=%CD%;tests;%OLD_PYTHONPATH%"
+  ) else (
+    set "PYTHONPATH=%CD%;tests"
+  )
+) else (
+  if defined OLD_PYTHONPATH (
+    set "PYTHONPATH=%CD%;%OLD_PYTHONPATH%"
+  ) else (
+    set "PYTHONPATH=%CD%"
+  )
+)
+pytest
+if errorlevel 1 set /a overall_ec=1
+set "PYTHONPATH=%OLD_PYTHONPATH%"
+popd >nul
+
+popd >nul
+:after
+rmdir /s /q "%PKGDIR%" >nul 2>&1
+goto :eof

requirements/packs/scripts/_pytest.sh

@@ -0,0 +1,64 @@
+#!/usr/bin/env bash
+# Usage:
+#   ./_pytest.sh urls.txt
+#   ./_pytest.sh https://host/a.tar.gz https://host/b.tgz
+# From ChatGPT
+
+set -euo pipefail
+
+URLS=()
+if (($# == 1)) && [ -f "$1" ]; then
+  URLS_FILE="$1"
+  case "$URLS_FILE" in /*) ;; *) URLS_FILE="$PWD/$URLS_FILE" ;; esac
+  while IFS= read -r line; do
+    [[ -z "${line// }" || "$line" =~ ^[[:space:]]*# ]] && continue
+    URLS+=("$line")
+  done < "$URLS_FILE"
+else
+  URLS=("$@")
+fi
+
+START_DIR="$PWD"
+TMPROOT="$(TMPDIR="$START_DIR" mktemp -d -t .tmp_remote_tests.XXXXXXXX)"
+trap 'cd "$START_DIR" 2>/dev/null || true; rm -rf -- "$TMPROOT"' EXIT
+cd "$TMPROOT"
+
+overall_ec=0
+i=0
+for url in "${URLS[@]}"; do
+  ((++i))
+  printf '\n==> [%d] %s\n' "$i" "$url"
+
+  tfile="$(TMPDIR="$TMPROOT" mktemp -t "dl_${i}.XXXXXXXX")"
+  tarball="${tfile}.tar.gz"
+  curl -L --fail -o "$tarball" "$url"
+
+  pkgdir="$TMPROOT/pkg_${i}"
+  mkdir -p "$pkgdir"
+  tar -xzf "$tarball" -C "$pkgdir" 2>/dev/null || tar -xf "$tarball" -C "$pkgdir"
+
+  first_entry="$(tar -tzf "$tarball" 2>/dev/null | head -1 || true)"
+  if [ -z "$first_entry" ]; then
+    first_entry="$(tar -tf "$tarball" 2>/dev/null | head -1 || true)"
+  fi
+
+  top="${first_entry%%/*}"
+  if [ -n "$top" ] && [ -d "$pkgdir/$top" ]; then
+    projroot="$pkgdir/$top"
+  else
+    projroot="$pkgdir"
+  fi
+
+  [ -d "$projroot/src" ] && rm -rf -- "$projroot/src"
+
+  if [ -d "$projroot/tests" ]; then
+    ( cd "$projroot" && PYTHONPATH="$PWD:tests:${PYTHONPATH:-}" pytest ) || overall_ec=1
+  else
+    ( cd "$projroot" && PYTHONPATH="$PWD:${PYTHONPATH:-}" pytest ) || overall_ec=1
+  fi
+
+  rm -f -- "$tarball" "$tfile"
+  rm -rf -- "$pkgdir"
+done
+
+exit "$overall_ec"

requirements/packs/scripts/tar_url.txt

@@ -0,0 +1,5 @@
+https://github.com/diffpy/diffpy.srreal/archive/refs/tags/1.4.0.tar.gz
+https://github.com/diffpy/diffpy.srfit/archive/refs/tags/3.2.0.tar.gz
+https://github.com/diffpy/pyobjcryst/archive/refs/tags/2025.1.0.tar.gz
+https://github.com/diffpy/diffpy.structure/archive/refs/tags/3.3.1.tar.gz
+https://github.com/Tieqiong/diffpy.utils/archive/refs/tags/3.6.2-rc.0.tar.gz

requirements/packs/tests.txt

@@ -0,0 +1,9 @@
+flake8
+pytest
+codecov
+coverage
+pytest-cov
+pytest-env
+pytest-mock
+freezegun
+DeepDiff

requirements/profiles/_tests.yml

@@ -0,0 +1,11 @@
+# script name must coincide with conda installation name
+# script named "_*" can escape install presence check
+
+packs:
+  - core
+  - pdf
+  - tests
+
+extras:
+  - _pytest.sh tar_url.txt
+  - _pytest.bat tar_url.txt

requirements/profiles/all.yml

@@ -0,0 +1,9 @@
+# all
+
+packs:
+  - core
+  - pdf
+  - plotting
+
+extras:
+  - ipykernel

requirements/tests.txt

@@ -1,6 +1,10 @@
+# temporary before updating skpkg release-scripts
 flake8
 pytest
 codecov
 coverage
 pytest-cov
 pytest-env
+pytest-mock
+freezegun
+DeepDiff