Check api and uq modules and circleCI and workflow updates

.circleci/config.yml

@@ -8,27 +8,73 @@ orbs:
 
 commands:
   install-miniconda:
-    description: Install Miniconda on machine executors (macOS only; Windows images ship with Miniconda)
+    description: Ensure conda is on PATH (install if missing on Windows/macOS)
     steps:
       - run:
           name: Install Miniconda
           command: |
             set -euo pipefail
+
+            conda_present_at() {
+              local root="$1"
+              [ -n "${root}" ] && { [ -f "${root}/Scripts/conda.exe" ] || [ -f "${root}/bin/conda" ]; }
+            }
+
             if command -v conda >/dev/null 2>&1; then
               echo "Conda already available at $(command -v conda)"
+              conda config --set quiet true
               conda --version
               exit 0
             fi
-            MINICONDA_DIR="${HOME}/miniconda3"
-            if [ -x "${MINICONDA_DIR}/Scripts/conda.exe" ] || [ -x "${MINICONDA_DIR}/bin/conda" ]; then
-              echo "Miniconda already present at ${MINICONDA_DIR}"
-            else
-              case "$(uname -s)" in
-                MINGW*|MSYS*|CYGWIN*)
-                  echo "install-miniconda: unexpected Windows path without preinstalled conda"
-                  exit 1
-                  ;;
-                Darwin)
+
+            MINICONDA_DIR=""
+            case "$(uname -s)" in
+              MINGW*|MSYS*|CYGWIN*)
+                for candidate in \
+                  "${CONDA:-}" \
+                  "/c/Miniconda" \
+                  "/c/Miniconda3" \
+                  "/c/ProgramData/miniconda3" \
+                  "/c/ProgramData/Miniconda3" \
+                  "${HOME}/miniconda3" \
+                  "${HOME}/Miniconda3" \
+                  "${HOME}/appdata/Local/miniconda3" \
+                  "${HOME}/appdata/Local/Continuum/miniconda3"; do
+                  if conda_present_at "${candidate}"; then
+                    MINICONDA_DIR="${candidate}"
+                    break
+                  fi
+                done
+
+                if [ -z "${MINICONDA_DIR}" ]; then
+                  conda_exe="$(cmd.exe //c "where conda 2>nul" 2>/dev/null | head -n1 | tr -d '\r' || true)"
+                  if [ -n "${conda_exe}" ]; then
+                    if command -v cygpath >/dev/null 2>&1; then
+                      conda_exe="$(cygpath -u "${conda_exe}")"
+                    else
+                      conda_exe="$(echo "${conda_exe}" | sed 's|\\|/|g' | sed 's|^\([A-Za-z]\):|/\L\1|')"
+                    fi
+                    MINICONDA_DIR="$(cd "$(dirname "${conda_exe}")/.." && pwd)"
+                  fi
+                fi
+
+                if [ -z "${MINICONDA_DIR}" ]; then
+                  MINICONDA_DIR="${HOME}/miniconda3"
+                fi
+
+                if ! conda_present_at "${MINICONDA_DIR}"; then
+                  echo "Installing Miniconda to %USERPROFILE%\\miniconda3 via cmd.exe..."
+                  curl -fsSL -o miniconda-installer.exe \
+                    "https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe"
+                  # /D= must be last and must not be quoted (NSIS installer requirement).
+                  cmd.exe //c "miniconda-installer.exe /InstallationType=JustMe /RegisterPython=0 /S /D=%USERPROFILE%\\miniconda3"
+                  rm -f miniconda-installer.exe
+                  MINICONDA_DIR="${HOME}/miniconda3"
+                fi
+                ;;
+              Darwin)
+                MINICONDA_DIR="${HOME}/miniconda3"
+                if ! conda_present_at "${MINICONDA_DIR}"; then
                   ARCH="$(uname -m)"
                   if [ "${ARCH}" = "arm64" ]; then
                     INSTALLER_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh"
@@ -38,13 +84,20 @@ commands:
                   curl -fsSL -o miniconda-installer.sh "${INSTALLER_URL}"
                   bash miniconda-installer.sh -b -p "${MINICONDA_DIR}"
                   rm -f miniconda-installer.sh
-                  ;;
-                *)
-                  echo "install-miniconda: unsupported OS $(uname -s)"
-                  exit 1
-                  ;;
-              esac
+                fi
+                ;;
+              *)
+                echo "install-miniconda: unsupported OS $(uname -s)"
+                exit 1
+                ;;
+            esac
+
+            if ! conda_present_at "${MINICONDA_DIR}"; then
+              echo "install-miniconda: conda not found under ${MINICONDA_DIR}"
+              exit 1
             fi
+            echo "Using Miniconda at ${MINICONDA_DIR}"
+
             {
               echo "export MINICONDA_DIR=${MINICONDA_DIR}"
               case "$(uname -s)" in
@@ -58,6 +111,7 @@ commands:
             } >> "${BASH_ENV}"
             # shellcheck source=/dev/null
             source "${BASH_ENV}"
+            conda config --set quiet true
             conda --version
 
   run-conda-test-suite:
@@ -75,8 +129,9 @@ commands:
             [ -f "${BASH_ENV}" ] && source "${BASH_ENV}"
 
             eval "$(conda shell.bash hook)"
-            conda update -y conda
-            conda create -n cheminf python=3.12 -y
+            conda config --set quiet true
+            conda update -y -q conda
+            conda create -n cheminf python=3.11 -y -q
             conda activate cheminf
 
             python -m pip install --upgrade pip
@@ -93,6 +148,7 @@ commands:
               Linux)
                 CONDA_PKGS+=(
                   libgfortran=14.2.0
+                  libgomp
                   libxkbcommon
                   mscorefonts
                   fonts-conda-forge
@@ -101,8 +157,20 @@ commands:
               Darwin)
                 CONDA_PKGS+=(libgfortran=14.2.0)
                 ;;
+              MINGW*|MSYS*|CYGWIN*)
+                # xTB on win-64 is built with MinGW; match Linux/macOS Fortran/OpenMP runtimes.
+                CONDA_PKGS+=(
+                  libgfortran=14.2.0
+                  llvm-openmp
+                )
+                ;;
             esac
-            conda install -y -c conda-forge "${CONDA_PKGS[@]}"
+            if ! conda install -y -q -c conda-forge "${CONDA_PKGS[@]}" >conda-install.log 2>&1; then
+              echo "conda install failed; last 200 lines:"
+              tail -n 200 conda-install.log
+              exit 1
+            fi
+            echo "conda install finished ($(wc -c < conda-install.log) bytes of log)"
 
             case "$(uname -s)" in
               Linux)
@@ -120,6 +188,76 @@ commands:
             pip install .
             pip install pytest pytest-cov pytest-qt
 
+            # xtb needs OpenMP/Fortran runtimes from the conda env (verify before AQME tests).
+            case "$(uname -s)" in
+              Linux)
+                export LD_LIBRARY_PATH="$CONDA_PREFIX/lib:${LD_LIBRARY_PATH:-}"
+                ;;
+              Darwin)
+                export DYLD_FALLBACK_LIBRARY_PATH="$CONDA_PREFIX/lib:${DYLD_FALLBACK_LIBRARY_PATH:-}"
+                ;;
+              MINGW*|MSYS*|CYGWIN*)
+                export PATH="$CONDA_PREFIX/Library/bin:$CONDA_PREFIX/Scripts:$PATH"
+                ;;
+            esac
+            command -v xtb
+            xtb --version
+            python -c "import importlib.metadata as m; import aqme; print('aqme', m.version('aqme'))"
+            # Windows-only preflight: Linux/macOS AQME tests already pass in CI.
+            case "$(uname -s)" in
+              MINGW*|MSYS*|CYGWIN*)
+                conda list | grep -E '^(xtb|aqme|libgfortran|libgomp|llvm-openmp)\s' || true
+                echo "=== Windows AQME/xTB preflight ==="
+                PREFLIGHT_DIR="$(mktemp -d)"
+                printf '%s\n' \
+                  '3' \
+                  'preflight' \
+                  'C   0.000000   0.000000   0.000000' \
+                  'H   1.089000   0.000000   0.000000' \
+                  'H  -0.363000   1.028000   0.000000' \
+                  > "${PREFLIGHT_DIR}/preflight.xyz"
+                set +e
+                xtb_out="$(xtb "${PREFLIGHT_DIR}/preflight.xyz" --gfn 2 --chrg 0 --uhf 0 2>&1)"
+                xtb_rc=$?
+                set -e
+                echo "${xtb_out}" | tail -n 40
+                if [ "${xtb_rc}" -ne 0 ]; then
+                  echo "xtb preflight failed (exit ${xtb_rc})"
+                  exit 1
+                fi
+                if ! echo "${xtb_out}" | grep -qiE 'total energy|:: total energy'; then
+                  echo "xtb preflight: no energy line in output"
+                  exit 1
+                fi
+
+                printf 'code_name,SMILES\npreflight,C\n' > "${PREFLIGHT_DIR}/AQME_indiv.csv"
+                (
+                  cd "${PREFLIGHT_DIR}"
+                  python -u -m aqme --qdescp \
+                    --input AQME_indiv.csv \
+                    --program xtb \
+                    --csv_name AQME_indiv.csv \
+                    --nprocs 1 \
+                    --sample 1 \
+                    --robert
+                )
+                if [ ! -f "${PREFLIGHT_DIR}/AQME-ROBERT_interpret_AQME_indiv.csv" ]; then
+                  echo "AQME preflight: expected CSV not created"
+                  ls -la "${PREFLIGHT_DIR}" || true
+                  for log in "${PREFLIGHT_DIR}/QDESCP/QDESCP_data.dat" \
+                             "${PREFLIGHT_DIR}/CSEARCH/CSEARCH_data.dat"; do
+                    if [ -f "${log}" ]; then
+                      echo "--- tail ${log} ---"
+                      tail -n 80 "${log}"
+                    fi
+                  done
+                  exit 1
+                fi
+                echo "Windows AQME/xTB preflight passed"
+                rm -rf "${PREFLIGHT_DIR}"
+                ;;
+            esac
+
             set +e
 
             python -m pytest \
@@ -279,6 +417,7 @@ jobs:
     shell: bash.exe
     steps:
       - checkout
+      - install-miniconda
       - run-conda-test-suite:
           upload_coverage: false
 

.gitignore

@@ -131,3 +131,14 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# ROBERT module run outputs (local working directory artifacts)
+CURATE/
+GENERATE/
+VERIFY/
+PREDICT/
+AQME/
+EVALUATE/
+ROBERT_report.pdf
+report_debug.txt
+report.css

README.md

@@ -15,7 +15,7 @@ Full documentation with installation instructions, technical details and example
 Don't miss out the latest hands-on tutorials from our [YouTube channel](https://www.youtube.com/channel/UCHRqI8N61bYxWV9BjbUI4Xw)!
 
 ## Recommended installation
-1. (Only once) Create new conda environment: `conda create -n robert python=3.10`  
+1. (Only once) Create new conda environment: `conda create -n robert python=3.12`  
 2. Activate conda environment: `conda activate robert`  
 3. Install ROBERT using pip: `pip install robert`
 4. Install RDKit (only if you plan to use easyROB): `pip install rdkit`

build_easyrob/config_files/backend_env.yaml

@@ -13,5 +13,5 @@ dependencies:
   - mscorefonts
   - pip
   - pip:
-      - robert==2.0.2
+      - robert==2.2.0
       - aqme==2.0.0

docs/Examples/full_workflow/CSV/Robert_example.csv

@@ -1,6 +1,38 @@
 Name,Target_values,x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11
 1,1.854766065,12,110.9270401,70.8240401,Csub-H,89.87553406,49.77253406,1,0,0,0,1
 2,2.034511341,11.7,110.6553116,70.25231158,Csub-Csub,78.65235138,55.53135138,1,0,0,0,1
-..., , , , , , , , , , , , 
+3,0.860667495,-23.05,112.0635071,36.91050708,H-O,88.85021973,13.69721973,0,0,1,1,1
+4,1.026447198,-16.24,112.101181,43.75818103,Csub-O,69.10329437,18.04229437,0,1,0,1,1
+5,0.952469022,-31.94,111.8824539,27.83945392,H-O,88.58656311,4.54356311,1,0,1,1,2
+6,0.308776518,-68.04,113.0647278,-7.078272217,H-O,89.46292114,-30.68007886,0,0,2,2,2
+7,0.982261986,-34.71,110.7689209,23.9559209,Csub-Csub,79.076828,9.545828003,1,0,1,1,2
+8,1.129601283,-34.94,111.5555725,24.51257251,Csub-Csub,78.75331879,8.992318787,1,0,1,1,2
+9,1.047746118,-34.48,110.5679703,23.98497028,Csub-Csub,78.03665161,8.735651611,1,0,1,1,2
+10,0.515551116,-62.34,110.4608917,-3.982108276,Csub-O,58.43679047,-38.72420953,0,1,1,2,2
+11,0.515551116,-62.34,113.9221497,-0.520850342,Csub-O,69.55827332,-27.60272668,0,1,1,2,2
+12,0.44305174,-62.34,112.8844147,-1.558585327,Csub-O,62.99021912,-34.17078088,0,1,1,2,2
+13,2.221390241,0.29,110.5127563,58.69975635,Csub-Csub,77.87947083,43.34847083,2,0,0,0,2
+14,2.138192104,-0.78,110.3923798,57.50937976,Csub-Csub,78.41550446,42.81450446,2,0,0,0,2
+15,1.883806797,4.54,110.719635,63.15663501,Csub-H,89.83821106,42.27521106,2,0,0,0,2
+16,2.091025544,4.12,111.3189087,63.33590869,Csub-H,89.78244019,41.79944019,2,0,0,0,2
+17,1.902644865,4.29,110.7536316,62.94063159,Csub-H,89.6808548,41.8678548,2,0,0,0,2
+18,2.312908191,-0.46,110.959137,58.39613696,Csub-Csub,78.64178467,43.36078467,2,0,0,0,2
+19,1.16234335,-30.93,110.8476944,27.8146944,Csub-Csub,76.10786438,10.35686438,1,0,0,0,1
+20,1.989080521,-32.41,111.2339783,26.72097827,Csub-H,82.79759216,5.392952454,2,0,0,0,2
+21,2.801329141,-5.9,110.3707199,52.36771991,Csub-Csub,78.09907532,37.37807532,2,0,0,0,2
+22,2.391560251,-5.9,110.9408264,52.93782642,Csub-Csub,78.66916656,37.94816656,2,0,0,0,2
+23,2.011592734,-5.9,110.4220352,52.41903522,Csub-Csub,78.39561462,37.67461462,2,0,0,0,2
+24,0.998633019,-27.6,110.4682465,30.76524646,Csub-O,66.3848114,3.963811401,1,1,0,1,2
+25,1.031375085,-27.6,113.392807,33.68980701,Csub-O,69.00031281,6.579312805,1,1,0,1,2
+26,1.006818535,-27.6,112.2061539,32.50315387,Csub-O,67.16915131,4.748151306,1,1,0,1,2
+27,1.694401925,-29.7,110.9802704,29.17727039,Csub-Csub,77.10182953,51.03182953,1,0,0,0,1
+28,0.515838419,-65.68,111.9355087,-5.847491272,H-O,78.45265198,-39.33034802,0,0,2,2,2
+29,0.916777853,-24.3,111.7115936,35.30859363,Csub-O,70.3069458,17.6069458,0,1,0,1,1
+30,0.837770564,-71.32,111.7983551,-11.6246449,H-O,76.89291382,-46.53008618,1,0,2,2,3
+31,0.942297022,-30.67,111.0540771,28.28107715,H-O,86.16723633,3.394236328,1,0,1,1,2
+32,0.965415203,-29.94,110.8601837,28.81718372,H-O,86.97593689,4.93293689,1,0,1,1,2
+33,0.39762592,-101.6,111.0383148,-42.66468518,Csub-O,55.76971817,-71.26043939,0,2,1,3,3
+34,1.178714383,-101.6,111.0308151,-42.67218488,H-O,84.12934875,-69.57365125,2,0,1,1,3
+35,0.410599034,-101.6,111.6276932,-42.07530682,Csub-O,59.93067169,-76.49032831,0,2,1,3,3
 36,0.321084552,-101.6,110.7593079,-42.94369214,Csub-O,59.81459808,-76.60640192,0,2,1,3,3
 37,0.329517076,-101.6,115.2292938,-38.47370618,Csub-O,70.45233154,-65.96866846,0,2,1,3,3

docs/Examples/full_workflow/full_workflow.rst

@@ -49,11 +49,19 @@ Executing the job
 Execution time and versions
 +++++++++++++++++++++++++++
 
-Time: ~3.5 min
+Time: ~10 min
 
-System: 8 processors (11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz) using 16.0 GB RAM memory
+System: 8 processors (x86_64 Linux) using 16.0 GB RAM memory
 
-ROBERT version: 2.0.1
+ROBERT version: 2.2.0
+
+numpy version: 2.3.4
+
+scikit-learn version: 1.7.2
+
+xgboost version: 2.1.4
+
+bayesian-optimization version: 3.1.0
 
 scikit-learn-intelex version: 2025.2.0
 

docs/Examples/full_workflow/full_workflow_test.rst

@@ -49,11 +49,19 @@ Executing the job
 Execution time and versions
 +++++++++++++++++++++++++++
 
-Time: ~10 sec
+Time: ~1.5 min
 
-System: 8 processors (11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz) using 16.0 GB RAM memory
+System: 8 processors (x86_64 Linux) using 16.0 GB RAM memory
 
-ROBERT version: 2.0.1
+ROBERT version: 2.2.0
+
+numpy version: 2.3.4
+
+scikit-learn version: 1.7.2
+
+xgboost version: 2.1.4
+
+bayesian-optimization version: 3.1.0
 
 scikit-learn-intelex version: 2025.2.0
 

docs/Examples/full_workflow/smiles_vaskas.rst

@@ -148,15 +148,23 @@ Execution time and versions
 
 Time: ~3 min
 
-System: 4 processors (Intel Xeon Ice Lake 8352Y) using 8.0 GB RAM memory
+System: 8 processors (x86_64 Linux) using 16.0 GB RAM memory
 
-ROBERT version: 1.2.0
+ROBERT version: 2.2.0
 
-scikit-learn-intelex version: 2024.5.0
+numpy version: 2.3.4
 
-AQME version: 1.6.1
+scikit-learn version: 1.7.2
 
-xTB version: 6.6.1
+xgboost version: 2.1.4
+
+bayesian-optimization version: 3.1.0
+
+scikit-learn-intelex version: 2025.2.0
+
+AQME version: 2.0.0
+
+xTB version: 6.7.1
 
 Results
 +++++++