Fix CI configuration by adding missing environment files and correcting directory references

asap_env.yaml

@@ -0,0 +1,30 @@
+name: asap_env
+channels:
+  - conda-forge
+  - fastai
+dependencies:
+  - python=3.10
+  - pip
+  - setuptools
+  # Core Library Dependencies
+  - fastcore>=1.5
+  - numpy
+  - scipy
+  - ase
+  - spglib
+  - tqdm
+  - click
+  - matplotlib
+  - ipython
+  # Domain Specific (including asap3 and openkim-models for ASAP tests)
+  - alamode
+  - openkim-models=2021.01.28
+  - asap3
+  # Development Tools
+  - nbdev
+  - jupyterlab
+  - ipywidgets
+  - pre-commit
+  - quarto
+  - pip:
+    - -e .

nbs/01_VASP_Tutorial.ipynb

@@ -106,7 +106,7 @@
    "source": [
     "#| vasp\n",
     "# Directory in which our project resides\n",
-    "base_dir = f'../example/VASP_3C-SiC/{supercell}/'"
+    "base_dir = f'../examples/VASP_3C-SiC/{supercell}/'"
    ]
   },
   {
@@ -158,7 +158,7 @@
     "# Setup the calculator - single point energy calculation\n",
     "# The details will change here from case to case\n",
     "# We are using run-calc.sh from the main project directory!\n",
-    "calc.set(directory=f'../TMP/calc_{supercell}/sc')\n",
+    "calc.set(directory=f'../.tmp/calc_{supercell}/sc')\n",
     "calc.set(command=f'{os.getcwd()}/../run-calc.sh \"3C-SiC-{supercell}\"')\n",
     "calc.set(nsw=0)\n",
     "cryst.calc = calc"
@@ -214,7 +214,7 @@
     "#|vasp\n",
     "# Space for results\n",
     "xsl = []\n",
-    "calc_dir = f'../TMP/calc_{supercell}'"
+    "calc_dir = f'../.tmp/calc_{supercell}'"
    ]
   },
   {

nbs/02_CLI.ipynb

@@ -74,12 +74,12 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.makedirs('TMP', exist_ok=True)\n",
+    "os.makedirs('.tmp', exist_ok=True)\n",
     "#| hide\n",
     "#| vasp\n",
     "from tempfile import TemporaryDirectory\n",
-    "calc_dir = TemporaryDirectory(dir='../TMP')\n",
-    "calc_dir_2 = TemporaryDirectory(dir='../TMP')"
+    "calc_dir = TemporaryDirectory(dir='../.tmp')\n",
+    "calc_dir_2 = TemporaryDirectory(dir='../.tmp')"
    ]
   },
   {
@@ -484,12 +484,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "$ hecss-sampler -W ../TMP/tmp552lh_fn -T 1000 -N 0 -e 10 -k 0 -c ./run-calc.sh ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "$ hecss-sampler -W ../.tmp/tmp552lh_fn -T 1000 -N 0 -e 10 -k 0 -c ./run-calc.sh ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "\n",
       "HECSS (0.5.29)\n",
-      "Supercell:      ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "Supercell:      ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "Temperature:    1000.0K\n",
-      "Work directory: ../TMP/tmp552lh_fn\n",
+      "Work directory: ../.tmp/tmp552lh_fn\n",
       "Calculator:     VASP\n",
       "\n",
       "<Result RuntimeError('Looking for PP for potpaw/C/POTCAR\\n                        The pseudopotentials are expected to be in:\\n                        LDA:  $VASP_PP_PATH/potpaw/\\n                        PBE:  $VASP_PP_PATH/potpaw_PBE/\\n                        PW91: $VASP_PP_PATH/potpaw_GGA/\\n\\n                        No pseudopotential for C!')>\n"
@@ -536,7 +536,7 @@
     "            \"-T 1000 -N 0 -e 10 \"\n",
     "            \"-k 0 \"\n",
     "            \"-c ./run-calc.sh \"\n",
-    "            \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
+    "            \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
    ]
   },
   {
@@ -557,12 +557,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "$ hecss-sampler -W ../TMP/tmp552lh_fn -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "$ hecss-sampler -W ../.tmp/tmp552lh_fn -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "\n",
       "HECSS (0.5.29)\n",
-      "Supercell:      ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "Supercell:      ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "Temperature:    300.0K\n",
-      "Work directory: ../TMP/tmp552lh_fn\n",
+      "Work directory: ../.tmp/tmp552lh_fn\n",
       "Calculator:     VASP\n",
       "\n",
       "<Result RuntimeError('Looking for PP for potpaw/C/POTCAR\\n                        The pseudopotentials are expected to be in:\\n                        LDA:  $VASP_PP_PATH/potpaw/\\n                        PBE:  $VASP_PP_PATH/potpaw_PBE/\\n                        PW91: $VASP_PP_PATH/potpaw_GGA/\\n\\n                        No pseudopotential for C!')>\n"
@@ -613,7 +613,7 @@
     "            \"-T 300 -N 10 -w 1.85 \"\n",
     "            \"-c ./run-calc.sh \"\n",
     "            \"-s scale.dat \"\n",
-    "            \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
+    "            \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
    ]
   },
   {
@@ -675,11 +675,11 @@
       "  -V, --version       Show the version and exit.\n",
       "  -h, --help          Show this message and exit.\n",
       "\n",
-      "$ calculate-xscale -o ../TMP/tmp552lh_fn/iscale.dat -s 10 ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR ../TMP/tmp552lh_fn/T_300.0K/scale.dat\n",
+      "$ calculate-xscale -o ../.tmp/tmp552lh_fn/iscale.dat -s 10 ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR ../.tmp/tmp552lh_fn/T_300.0K/scale.dat\n",
       "\n",
       "Usage: calculate-xscale [OPTIONS] SUPERCELL SCALE\n",
       "\n",
-      "Error: Invalid value for 'SCALE': Path '../TMP/tmp552lh_fn/T_300.0K/scale.dat' does not exist.\n",
+      "Error: Invalid value for 'SCALE': Path '../.tmp/tmp552lh_fn/T_300.0K/scale.dat' does not exist.\n",
       "\n",
       "<Result SystemExit(2)>\n"
      ]
@@ -703,7 +703,7 @@
     "run_cli_cmd(calculate_xscale, \"--help\")\n",
     "run_cli_cmd(calculate_xscale, \n",
     "            f\"-o {calc_dir.name}/iscale.dat -s 10 \"\n",
-    "            \"../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR \"\n",
+    "            \"../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR \"\n",
     "            f\"{calc_dir.name}/T_300.0K/scale.dat\")"
    ]
   },
@@ -723,12 +723,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "$ hecss-sampler -W ../TMP/tmpgf1xuhq8 -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat -a ../TMP/tmp552lh_fn/iscale.dat ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "$ hecss-sampler -W ../.tmp/tmpgf1xuhq8 -T 300 -N 10 -w 1.85 -c ./run-calc.sh -s scale.dat -a ../.tmp/tmp552lh_fn/iscale.dat ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "\n",
       "HECSS (0.5.29)\n",
-      "Supercell:      ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
+      "Supercell:      ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\n",
       "Temperature:    300.0K\n",
-      "Work directory: ../TMP/tmpgf1xuhq8\n",
+      "Work directory: ../.tmp/tmpgf1xuhq8\n",
       "Calculator:     VASP\n",
       "\n",
       "<Result RuntimeError('Looking for PP for potpaw/C/POTCAR\\n                        The pseudopotentials are expected to be in:\\n                        LDA:  $VASP_PP_PATH/potpaw/\\n                        PBE:  $VASP_PP_PATH/potpaw_PBE/\\n                        PW91: $VASP_PP_PATH/potpaw_GGA/\\n\\n                        No pseudopotential for C!')>\n"
@@ -778,7 +778,7 @@
     "run_cli_cmd(hecss_sampler, \n",
     "            f\"-W {calc_dir_2.name} -T 300 -N 10 -w 1.85 \"\n",
     "            f\"-c ./run-calc.sh -s scale.dat -a {calc_dir.name}/iscale.dat\"\n",
-    "            \" ../example/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
+    "            \" ../examples/VASP_3C-SiC/1x1x1/sc_1x1x1/CONTCAR\")"
    ]
   },
   {
@@ -855,8 +855,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "cat: '../TMP/$../TMP/tmp552lh_fn/T_300.0K/DFSET.dat.raw': Nie ma takiego pliku ani katalogu\n",
-      "cat: '../TMP/$../TMP/tmpgf1xuhq8/T_300.0K/DFSET.dat.raw': Nie ma takiego pliku ani katalogu\n",
+      "cat: '../.tmp/$../.tmp/tmp552lh_fn/T_300.0K/DFSET.dat.raw': Nie ma takiego pliku ani katalogu\n",
+      "cat: '../.tmp/$../.tmp/tmpgf1xuhq8/T_300.0K/DFSET.dat.raw': Nie ma takiego pliku ani katalogu\n",
       "$ reshape-sample --help\n",
       "\n",
       "Usage: reshape-sample [OPTIONS] DFSET [T]\n",
@@ -886,9 +886,9 @@
       "  -V, --version       Show the version and exit.\n",
       "  --help              Show this message and exit.\n",
       "\n",
-      "$ reshape-sample  -d -o ../TMP/DFSET.dat ../TMP/DFSET_raw.dat\n",
+      "$ reshape-sample  -d -o ../.tmp/DFSET.dat ../.tmp/DFSET_raw.dat\n",
       "\n",
-      "/home/jochym/Projects/hecss_AG/hecss/util.py:96: UserWarning: loadtxt: input contained no data: \"../TMP/DFSET_raw.dat\"\n",
+      "/home/jochym/Projects/hecss_AG/hecss/util.py:96: UserWarning: loadtxt: input contained no data: \"../.tmp/DFSET_raw.dat\"\n",
       "  dfset = loadtxt(fn).reshape(N,-1,6)\n",
       "\n",
       "<Result ValueError('cannot reshape array of size 0 into shape (0,newaxis,6)')>\n"
@@ -915,12 +915,12 @@
    ],
    "source": [
     "#| echo: false\n",
-    "!cat ../TMP/${calc_dir.name}/T_300.0K/DFSET.dat.raw ../TMP/${calc_dir_2.name}/T_300.0K/DFSET.dat.raw > ../TMP/DFSET_raw.dat\n",
-    "!rm -f ../TMP/DFSET.dat\n",
+    "!cat ../.tmp/${calc_dir.name}/T_300.0K/DFSET.dat.raw ../.tmp/${calc_dir_2.name}/T_300.0K/DFSET.dat.raw > ../.tmp/DFSET_raw.dat\n",
+    "!rm -f ../.tmp/DFSET.dat\n",
     "run_cli_cmd(reshape_sample, \"--help\")\n",
     "run_cli_cmd(reshape_sample, \n",
-    "            \" -d -o ../TMP/DFSET.dat\"\n",
-    "            \" ../TMP/DFSET_raw.dat\")"
+    "            \" -d -o ../.tmp/DFSET.dat\"\n",
+    "            \" ../.tmp/DFSET_raw.dat\")"
    ]
   },
   {
@@ -932,12 +932,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "$ reshape-sample  -N 1 -w -d -o ../TMP/tmp552lh_fn/T_300.0K/DFSET.dat --check ../TMP/tmp552lh_fn/T_300.0K/smpl ../TMP/tmp552lh_fn/T_300.0K/DFSET.dat.raw\n",
+      "$ reshape-sample  -N 1 -w -d -o ../.tmp/tmp552lh_fn/T_300.0K/DFSET.dat --check ../.tmp/tmp552lh_fn/T_300.0K/smpl ../.tmp/tmp552lh_fn/T_300.0K/DFSET.dat.raw\n",
       "\n",
       "Usage: reshape-sample [OPTIONS] DFSET [T]\n",
       "Try 'reshape-sample --help' for help.\n",
       "\n",
-      "Error: Invalid value for 'DFSET': Path '../TMP/tmp552lh_fn/T_300.0K/DFSET.dat.raw' does not exist.\n",
+      "Error: Invalid value for 'DFSET': Path '../.tmp/tmp552lh_fn/T_300.0K/DFSET.dat.raw' does not exist.\n",
       "\n",
       "<Result SystemExit(2)>\n"
      ]
@@ -1043,9 +1043,9 @@
       "  -V, --version       Show the version and exit.\n",
       "  --help              Show this message and exit.\n",
       "\n",
-      "$ plot-stats -n -w 7 -h 4 ../TMP/DFSET_raw.dat 300\n",
+      "$ plot-stats -n -w 7 -h 4 ../.tmp/DFSET_raw.dat 300\n",
       "\n",
-      "/home/jochym/Projects/hecss_AG/hecss/util.py:96: UserWarning: loadtxt: input contained no data: \"../TMP/DFSET_raw.dat\"\n",
+      "/home/jochym/Projects/hecss_AG/hecss/util.py:96: UserWarning: loadtxt: input contained no data: \"../.tmp/DFSET_raw.dat\"\n",
       "  dfset = loadtxt(fn).reshape(N,-1,6)\n",
       "\n",
       "<Result ValueError('cannot reshape array of size 0 into shape (0,newaxis,6)')>\n"
@@ -1080,7 +1080,7 @@
     "run_cli_cmd(plot_stats, \n",
     "            \"-n \" \n",
     "            \"-w 7 -h 4 \"\n",
-    "            \"../TMP/DFSET_raw.dat \"\n",
+    "            \"../.tmp/DFSET_raw.dat \"\n",
     "            \"300\")"
    ]
   },
@@ -1134,7 +1134,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "$ plot-stats -n -w 7 -h 4 ../example/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat 1200\n",
+      "$ plot-stats -n -w 7 -h 4 ../examples/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat 1200\n",
       "\n",
       "\n"
      ]
@@ -1155,7 +1155,7 @@
     "run_cli_cmd(plot_stats, \n",
     "               \"-n \" \n",
     "               \"-w 7 -h 4 \"\n",
-    "               \"../example/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat \"\n",
+    "               \"../examples/VASP_3C-SiC_calculated/2x2x2/T_1200K/DFSET.dat \"\n",
     "               \"1200\")"
    ]
   },
@@ -1253,7 +1253,7 @@
       "  -V, --version       Show the version and exit.\n",
       "  --help              Show this message and exit.\n",
       "\n",
-      "$ plot-bands -w 7 -h 4 -l '300K,600K,3000K' ../example/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands ../example/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands ../example/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \n",
+      "$ plot-bands -w 7 -h 4 -l '300K,600K,3000K' ../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands ../examples/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands ../examples/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \n",
       "\n",
       "\n"
      ]
@@ -1274,9 +1274,9 @@
     "run_cli_cmd(plot_bands, \"--help\")\n",
     "run_cli_cmd(plot_bands, \n",
     "               \"-w 7 -h 4 -l '300K,600K,3000K' \"\n",
-    "               \"../example/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands \"\n",
-    "               \"../example/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands \"\n",
-    "               \"../example/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \")"
+    "               \"../examples/VASP_3C-SiC_calculated/2x2x2/T_300K/phon/cryst.bands \"\n",
+    "               \"../examples/VASP_3C-SiC_calculated/2x2x2/T_600K/phon/cryst.bands \"\n",
+    "               \"../examples/VASP_3C-SiC_calculated/2x2x2/T_3000K/phon/cryst.bands \")"
    ]
   },
   {

nbs/03_monitor_stats.ipynb

@@ -74,7 +74,7 @@
    "source": [
     "T = 300\n",
     "supercell = '2x2x2'\n",
-    "plot_stats(load_dfset(f'../example/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat'), \n",
+    "plot_stats(load_dfset(f'../examples/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat'), \n",
     "           T=T, sqrN=True);"
    ]
   },
@@ -108,7 +108,7 @@
     "T = 600\n",
     "supercell = '1x1x1'\n",
     "monitor_stats(T=T, \n",
-    "              dfset=f'../example/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat',\n",
+    "              dfset=f'../examples/VASP_3C-SiC_calculated/{supercell}/T_{T:.0f}K/DFSET.dat',\n",
     "              once=True # Show the plot and exit\n",
     "             )"
    ]
@@ -146,7 +146,7 @@
     "fig, axs = plt.subplots(4,2, figsize=(14,14))\n",
     "\n",
     "for n, d in enumerate(sorted(\n",
-    "                glob('../example/VASP_3C-SiC_calculated/?x?x?/T_*K'), \n",
+    "                glob('../examples/VASP_3C-SiC_calculated/?x?x?/T_*K'), \n",
     "                key=lambda s: (s.split('/')[-2],float(s.split('/')[-1][2:-1])))):\n",
     "    T=float(d.split('/')[-1][2:-1])\n",
     "    sc = d.split('/')[-2]\n",

nbs/04_monitor_phonons.ipynb

@@ -59,7 +59,7 @@
     "for sc, ax in zip(('1x1x1', '2x2x2'), axs):\n",
     "    plt.sca(ax)\n",
     "    for T in 300, 600, 1200, 3000:\n",
-    "        plot_bands_file(f'../example/VASP_3C-SiC_calculated/{sc}/T_{T}K/phon/cryst.bands', lbl=f'T={T}K')\n",
+    "        plot_bands_file(f'../examples/VASP_3C-SiC_calculated/{sc}/T_{T}K/phon/cryst.bands', lbl=f'T={T}K')\n",
     "    plt.legend()\n",
     "    plt.title(f'Supercell: {sc}');"
    ]
@@ -84,7 +84,7 @@
     "#| interactive\n",
     "T = 3000\n",
     "supercell = '2x2x2'\n",
-    "monitor_phonons(directory=f'../example/VASP_3C-SiC_calculated/{supercell}/phon/', \n",
+    "monitor_phonons(directory=f'../examples/VASP_3C-SiC_calculated/{supercell}/phon/', \n",
     "                dfset=f'../T_3000K/DFSET.dat', \n",
     "                kpath='3C_SiC', charge='3C_SiC', sc=f'../sc/CONTCAR',\n",
     "                order=1,     # Change to 2 if you want to monitor cubic potential\n",

nbs/05_vasp_workflow.ipynb

@@ -97,8 +97,8 @@
    "source": [
     "#|vasp\n",
     "# Directory in which our project resides\n",
-    "base_dir = f'../example/VASP_3C-SiC/{supercell}/'\n",
-    "calc_dir = TemporaryDirectory(dir='../TMP')"
+    "base_dir = f'../examples/VASP_3C-SiC/{supercell}/'\n",
+    "calc_dir = TemporaryDirectory(dir='../.tmp')"
    ]
   },
   {