Repository: HaoZeke/wailord (language: python)

Issue:
ENH: Kill Konfik
- [konfik](https://github.com/rednafi/konfik) is gone


Discussion / hints:

Fix patch:
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..16ef5c5
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,3 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+
diff --git a/.github/workflows/build_wailord.yml b/.github/workflows/build_wailord.yml
index 39ee389..4bbce06 100644
--- a/.github/workflows/build_wailord.yml
+++ b/.github/workflows/build_wailord.yml
@@ -5,22 +5,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
-        poetry-version: [1.0, 1.1.2]
+        python-version: [3.9, 3.12]
         os: [ubuntu-18.04, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Setup PDM
+        uses: pdm-project/setup-pdm@v3
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Run image
-        uses: abatilo/actions-poetry@v2.0.0
-        with:
-          poetry-version: ${{ matrix.poetry-version }}
-      - name: Prep dependencies
-        run: poetry add twine && poetry install
+          cache: true
+          cache-dependency-path: |
+              ./pdm.lock
+              ./pdm.new.lock
+      - name: Install dependencies
+        run: pdm install -G:all
       - name: Test project
-        run: poetry run pytest
-      - name: Build project
-        run: poetry build
+        run: pdm run pytest
diff --git a/.gitignore b/.gitignore
index a25eaf9..d824152 100644
--- a/.gitignore
+++ b/.gitignore
@@ -496,3 +496,4 @@ TSWLatexianTemp*
 
 # End of https://www.toptal.com/developers/gitignore/api/tex
 
+/.pdm-python
diff --git a/HISTORY.rst b/HISTORY.rst
index ad48b06..e316c27 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,11 @@
 History
 =======
 
+0.1.0 (2023-11-15)
+------------------
+* Rewritten from scratch
+* Less dependencies
+
 0.0.2 (2020-12-27)
 ------------------
 
diff --git a/docs/conf.py b/docs/conf.py
index 559c9ad..fb1f127 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -43,7 +43,6 @@
     "sphinx.ext.mathjax",  # Need math support
     "sphinx.ext.githubpages",  # Puts the .nojekyll and CNAME files
     "sphinxcontrib.apidoc",  # Automatically sets up sphinx-apidoc
-    "sphinx_proof",  # Future proofing
     "sphinx_copybutton",  # Let there be plagiarism!
     "sphinx_sitemap",  # Always a good idea
     "sphinx_togglebutton",  # Toggles reduce clutter
@@ -211,7 +210,7 @@
         "Wailord Documentation",
         author,
         "wailord",
-        "One line description of project.",
+        "ORCA input generator and output parser.",
         "Miscellaneous",
     ),
 ]
diff --git a/docs/installation.rst b/docs/installation.rst
index 68cda89..e9b7a12 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -44,7 +44,7 @@ Once you have a copy of the source, you can install it with:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ pip install .
 
 
 .. _Github repo: https://github.com/HaoZeke/wailord
diff --git a/nix/sources.json b/nix/sources.json
deleted file mode 100644
index bce1712..0000000
--- a/nix/sources.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-    "niv": {
-        "branch": "master",
-        "description": "Easy dependency management for Nix projects",
-        "homepage": "https://github.com/nmattia/niv",
-        "owner": "nmattia",
-        "repo": "niv",
-        "rev": "9d35b9e4837ab88517210b1701127612c260eccf",
-        "sha256": "0q50xhnm8g2yfyakrh0nly4swyygxpi0a8cb9gp65wcakcgvzvdh",
-        "type": "tarball",
-        "url": "https://github.com/nmattia/niv/archive/9d35b9e4837ab88517210b1701127612c260eccf.tar.gz",
-        "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
-    },
-    "nixpkgs": {
-        "branch": "master",
-        "description": "Nix Packages collection",
-        "homepage": "",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "03dd1b355b6c7379500becdf170850a5a1dfea5a",
-        "sha256": "04qq8sy8nmh8mjdqqycgliqcfv7i5pb3vfigmn486qrrpazdf4g8",
-        "type": "tarball",
-        "url": "https://github.com/NixOS/nixpkgs/archive/03dd1b355b6c7379500becdf170850a5a1dfea5a.tar.gz",
-        "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
-    }
-}
diff --git a/nix/sources.nix b/nix/sources.nix
deleted file mode 100644
index b796fff..0000000
--- a/nix/sources.nix
+++ /dev/null
@@ -1,171 +0,0 @@
-# This file has been generated by Niv.
-
-let
-
-  #
-  # The fetchers. fetch_<type> fetches specs of type <type>.
-  #
-
-  fetch_file = pkgs: name: spec:
-    let
-      name' = sanitizeName name + "-src";
-    in
-      if spec.builtin or true then
-        builtins_fetchurl { inherit (spec) url sha256; name = name'; }
-      else
-        pkgs.fetchurl { inherit (spec) url sha256; name = name'; };
-
-  fetch_tarball = pkgs: name: spec:
-    let
-      name' = sanitizeName name + "-src";
-    in
-      if spec.builtin or true then
-        builtins_fetchTarball { name = name'; inherit (spec) url sha256; }
-      else
-        pkgs.fetchzip { name = name'; inherit (spec) url sha256; };
-
-  fetch_git = name: spec:
-    let
-      ref =
-        if spec ? ref then spec.ref else
-          if spec ? branch then "refs/heads/${spec.branch}" else
-            if spec ? tag then "refs/tags/${spec.tag}" else
-              abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!";
-    in
-      builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; };
-
-  fetch_local = spec: spec.path;
-
-  fetch_builtin-tarball = name: throw
-    ''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`.
-        $ niv modify ${name} -a type=tarball -a builtin=true'';
-
-  fetch_builtin-url = name: throw
-    ''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`.
-        $ niv modify ${name} -a type=file -a builtin=true'';
-
-  #
-  # Various helpers
-  #
-
-  # https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695
-  sanitizeName = name:
-    (
-      concatMapStrings (s: if builtins.isList s then "-" else s)
-        (
-          builtins.split "[^[:alnum:]+._?=-]+"
-            ((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name)
-        )
-    );
-
-  # The set of packages used when specs are fetched using non-builtins.
-  mkPkgs = sources: system:
-    let
-      sourcesNixpkgs =
-        import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; };
-      hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath;
-      hasThisAsNixpkgsPath = <nixpkgs> == ./.;
-    in
-      if builtins.hasAttr "nixpkgs" sources
-      then sourcesNixpkgs
-      else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then
-        import <nixpkgs> {}
-      else
-        abort
-          ''
-            Please specify either <nixpkgs> (through -I or NIX_PATH=nixpkgs=...) or
-            add a package called "nixpkgs" to your sources.json.
-          '';
-
-  # The actual fetching function.
-  fetch = pkgs: name: spec:
-
-    if ! builtins.hasAttr "type" spec then
-      abort "ERROR: niv spec ${name} does not have a 'type' attribute"
-    else if spec.type == "file" then fetch_file pkgs name spec
-    else if spec.type == "tarball" then fetch_tarball pkgs name spec
-    else if spec.type == "git" then fetch_git name spec
-    else if spec.type == "local" then fetch_local spec
-    else if spec.type == "builtin-tarball" then fetch_builtin-tarball name
-    else if spec.type == "builtin-url" then fetch_builtin-url name
-    else
-      abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}";
-
-  # If the environment variable NIV_OVERRIDE_${name} is set, then use
-  # the path directly as opposed to the fetched source.
-  replace = name: drv:
-    let
-      saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name;
-      ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}";
-    in
-      if ersatz == "" then drv else ersatz;
-
-  # Ports of functions for older nix versions
-
-  # a Nix version of mapAttrs if the built-in doesn't exist
-  mapAttrs = builtins.mapAttrs or (
-    f: set: with builtins;
-    listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set))
-  );
-
-  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295
-  range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1);
-
-  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257
-  stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1));
-
-  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269
-  stringAsChars = f: s: concatStrings (map f (stringToCharacters s));
-  concatMapStrings = f: list: concatStrings (map f list);
-  concatStrings = builtins.concatStringsSep "";
-
-  # https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331
-  optionalAttrs = cond: as: if cond then as else {};
-
-  # fetchTarball version that is compatible between all the versions of Nix
-  builtins_fetchTarball = { url, name ? null, sha256 }@attrs:
-    let
-      inherit (builtins) lessThan nixVersion fetchTarball;
-    in
-      if lessThan nixVersion "1.12" then
-        fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
-      else
-        fetchTarball attrs;
-
-  # fetchurl version that is compatible between all the versions of Nix
-  builtins_fetchurl = { url, name ? null, sha256 }@attrs:
-    let
-      inherit (builtins) lessThan nixVersion fetchurl;
-    in
-      if lessThan nixVersion "1.12" then
-        fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
-      else
-        fetchurl attrs;
-
-  # Create the final "sources" from the config
-  mkSources = config:
-    mapAttrs (
-      name: spec:
-        if builtins.hasAttr "outPath" spec
-        then abort
-          "The values in sources.json should not have an 'outPath' attribute"
-        else
-          spec // { outPath = replace name (fetch config.pkgs name spec); }
-    ) config.sources;
-
-  # The "config" used by the fetchers
-  mkConfig =
-    { sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null
-    , sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile)
-    , system ? builtins.currentSystem
-    , pkgs ? mkPkgs sources system
-    }: rec {
-      # The sources, i.e. the attribute set of spec name to spec
-      inherit sources;
-
-      # The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers
-      inherit pkgs;
-    };
-
-in
-mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); }
diff --git a/pdm.lock b/pdm.lock
new file mode 100644
index 0000000..5e4ce43
--- /dev/null
+++ b/pdm.lock
@@ -0,0 +1,1109 @@
+# This file is @generated by PDM.
+# It is not intended for manual editing.
+
+[metadata]
+groups = ["default", "docs", "lint", "test"]
+strategy = ["cross_platform"]
+lock_version = "4.4"
+content_hash = "sha256:6de3763fd8a640feb739920d28e1e3d1b950a98b6bd083de50888c362b0022f9"
+
+[[package]]
+name = "alabaster"
+version = "0.7.13"
+requires_python = ">=3.6"
+summary = "A configurable sidebar-enabled Sphinx theme"
+files = [
+    {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
+    {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
+]
+
+[[package]]
+name = "arrow"
+version = "1.3.0"
+requires_python = ">=3.8"
+summary = "Better dates & times for Python"
+dependencies = [
+    "python-dateutil>=2.7.0",
+    "types-python-dateutil>=2.8.10",
+]
+files = [
+    {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"},
+    {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"},
+]
+
+[[package]]
+name = "babel"
+version = "2.13.1"
+requires_python = ">=3.7"
+summary = "Internationalization utilities"
+dependencies = [
+    "setuptools; python_version >= \"3.12\"",
+]
+files = [
+    {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"},
+    {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"},
+]
+
+[[package]]
+name = "binaryornot"
+version = "0.4.4"
+summary = "Ultra-lightweight pure Python package to check if a file is binary or text."
+dependencies = [
+    "chardet>=3.0.2",
+]
+files = [
+    {file = "binaryornot-0.4.4-py2.py3-none-any.whl", hash = "sha256:b8b71173c917bddcd2c16070412e369c3ed7f0528926f70cac18a6c97fd563e4"},
+    {file = "binaryornot-0.4.4.tar.gz", hash = "sha256:359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061"},
+]
+
+[[package]]
+name = "certifi"
+version = "2023.7.22"
+requires_python = ">=3.6"
+summary = "Python package for providing Mozilla's CA Bundle."
+files = [
+    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
+    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+]
+
+[[package]]
+name = "chardet"
+version = "5.2.0"
+requires_python = ">=3.7"
+summary = "Universal encoding detector for Python 3"
+files = [
+    {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"},
+    {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+requires_python = ">=3.7.0"
+summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+files = [
+    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
+    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
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+    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
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+    {file = "charset_normalizer-3.3.2-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:802fe99cca7457642125a8a88a084cef28ff0cf9407060f7b93dca5aa25480db"},
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diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..4ca35d2
--- /dev/null
+++ b/pixi.toml
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+[project]
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diff --git a/poetry.lock b/poetry.lock
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index 68f5cf7..0000000
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diff --git a/pyproject.toml b/pyproject.toml
index c2fe46f..6a314e8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,72 +1,73 @@
-[tool.poetry]
+[project]
 name = "wailord"
-version = "0.0.2"
+version = "0.1.0"
 description = "Wailord is a python library to interact with ORCA"
-license = "GNU General Public License v3"
-authors = ["Rohit Goswami <rog32@hi.is>"]
-keywords = ["wailord", "quantum chemistry", "orca"]
-classifiers = ["Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8"]
-
-homepage = "https://wailord.xyz"
-repository = "https://github.com/HaoZeke/wailord"
-documentation = "https://wailord.xyz"
-
 readme = "README.rst"
+license = {text = "MIT"}
+authors = [
+    { name="Rohit Goswami", email="rgoswami@ieee.org" },
+]
+maintainers = [
+    { name="Rohit Goswami", email="rgoswami@ieee.org" },
+]
+keywords = ["wailord", "quantum chemistry", "orca"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "pint>=0.22",
+    "pint-pandas>=0.5",
+    "numpy>=1.26",
+    "pyyaml>=6.0.1",
+    "vg>=2.0.0",
+    "siuba>=0.4.4",
+    "parsimonious>=0.10.0",
+    "cookiecutter>=2.4.0",
+    "click>=8.1.7",
+]
 
-include = ["wailord_templates/**/*.*"]
-
-[tool.poetry.dependencies]
-python = "^3.7"
-click = ">=7.0"
-ase = "^3.20.1"
-pandas = "^1.1.3"
-parsimonious = "^0.8.1"
-konfik = "^2.0.0"
-cookiecutter = "^1.7.2"
-Jinja2 = "^2.11.2"
-black = "^20.8b1"
-flake8 = "^3.8.4"
-vg = "^1.9.0"
-Pint = "^0.16.1"
-Sphinx = "^3.3.1"
-sphinxcontrib-apidoc = "^0.3.0"
-sphinx-library = "^1.1.2"
-sphinx-autobuild = "^2020.9.1"
-sphinx-proof = "^0.0.3"
-sphinx-copybutton = "^0.3.1"
-sphinxcontrib-doxylink = "^1.6.1"
-sphinx-sitemap = "^2.2.0"
-sphinx-togglebutton = "^0.2.3"
-sphinx-comments = "^0.0.3"
-"sphinxcontrib.contributors" = "^1.0"
-sphinxcontrib-github_ribbon = "^0.9.0"
-sphinx-versions = "^1.1.3"
-sphinx-issues = "^1.2.0"
-sphinx-fasvg = "^0.1.3"
-sphinx-minipres = "^0.2.1"
-releases = "^1.6.3"
-Pint-Pandas = "^0.1"
-pytest-datadir = "^1.3.1"
-siuba = "^0.0.24"
-scipy = "^1.5.4"
-
-[tool.poetry.dev-dependencies]
-check-manifest = "*"
-pytest = "^4.6"
-
-[tool.poetry.extras]
-test = ["coverage", "pytest"]
+[project.urls]
+Homepage = "https://wailord.xyz"
+Repository = "https://github.com/HaoZeke/wailord"
+Documentation = "https://wailord.xyz"
 
 [build-system]
-requires = ["poetry_core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+[project.scripts]
+run = "wailord.cli:main"
 
-[tool.poetry.urls]
-"Bug Tracker" = "https://github.com/HaoZeke/wailord/issues"
+[tool.ruff]
+line-length = 80
+target-version = ['py310']
+select = [
+    "NPY",
+    "I",
+    "RUF",
+]
 
-[tool.poetry.scripts]
-run = "wailord.cli:main"
+[tool.pdm]
+[tool.pdm.dev-dependencies]
+lint = [
+    "ruff>=0.0.17",
+]
+docs = [
+    "sphinx>=7.1.2",
+    "sphinxcontrib-apidoc>=0.4.0",
+    "sphinx-copybutton>=0.5.2",
+    "sphinx-sitemap>=2.5.1",
+    "sphinx-togglebutton>=0.3.2",
+]
+test = [
+    "pytest>=7.4.3",
+    "pytest-datadir>=1.5.0",
+]
+
+[tool.pdm.scripts]
+lint = "ruff"
+all = {composite = ["lint wailord/"]}
 
-[tool.dephell.main]
-from = {format = "poetry", path = "pyproject.toml"}
-to = {format = "setuppy", path = "setup.py"}
diff --git a/wailord/__init__.py b/wailord/__init__.py
index 02c123e..e69de29 100644
--- a/wailord/__init__.py
+++ b/wailord/__init__.py
@@ -1,5 +0,0 @@
-"""Top-level package for Wailord."""
-
-__author__ = """Rohit Goswami"""
-__email__ = "rog32@hi.is"
-__version__ = "0.0.2"
diff --git a/wailord_templates/basicExperiment/cookiecutter.json b/wailord/_templates/basicExperiment/cookiecutter.json
similarity index 100%
rename from wailord_templates/basicExperiment/cookiecutter.json
rename to wailord/_templates/basicExperiment/cookiecutter.json
diff --git a/wailord_templates/basicExperiment/hooks/post_gen_project.py b/wailord/_templates/basicExperiment/hooks/post_gen_project.py
similarity index 92%
rename from wailord_templates/basicExperiment/hooks/post_gen_project.py
rename to wailord/_templates/basicExperiment/hooks/post_gen_project.py
index c0c5db1..e097d00 100755
--- a/wailord_templates/basicExperiment/hooks/post_gen_project.py
+++ b/wailord/_templates/basicExperiment/hooks/post_gen_project.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 
 import wailord.io as waio
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
 CUR = Path().absolute()
 
diff --git a/wailord_templates/basicExperiment/hooks/pre_gen_project.py b/wailord/_templates/basicExperiment/hooks/pre_gen_project.py
similarity index 100%
rename from wailord_templates/basicExperiment/hooks/pre_gen_project.py
rename to wailord/_templates/basicExperiment/hooks/pre_gen_project.py
diff --git a/wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/LICENSE b/wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/LICENSE
similarity index 100%
rename from wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/LICENSE
rename to wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/LICENSE
diff --git a/wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh b/wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh
similarity index 88%
rename from wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh
rename to wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh
index 87bf9b1..b47c778 100644
--- a/wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh
+++ b/wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/basejob.sh
@@ -45,6 +45,11 @@ echo "Scratchdir is: $tdir"
 
 $orcadir/orca orca.inp >orca.out
 
+# Check if SLURM_SUBMIT_DIR is set, if not set it to the script's directory
+if [ -z "$SLURM_SUBMIT_DIR" ]; then
+    SLURM_SUBMIT_DIR=$(dirname "$cur_dir")
+fi
+
 cp -r $tdir/*.xyz $SLURM_SUBMIT_DIR
 cp -r $tdir/*.gbw $SLURM_SUBMIT_DIR
 cp -r $tdir/*.out $SLURM_SUBMIT_DIR
diff --git a/wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/orca.yml b/wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/orca.yml
similarity index 100%
rename from wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/orca.yml
rename to wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/orca.yml
diff --git a/wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/readme.md b/wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/readme.md
similarity index 100%
rename from wailord_templates/basicExperiment/{{cookiecutter.project_slug}}/readme.md
rename to wailord/_templates/basicExperiment/{{cookiecutter.project_slug}}/readme.md
diff --git a/wailord/_utils.py b/wailord/_utils.py
new file mode 100644
index 0000000..dc1a3c6
--- /dev/null
+++ b/wailord/_utils.py
@@ -0,0 +1,69 @@
+from pathlib import Path
+
+
+def get_project_root() -> Path:
+    """
+    A helper to obtain the project root path
+    From here: https://stackoverflow.com/a/53465812/1895378
+    """
+    return Path(__file__).parent.parent
+
+
+def repkey(fname, repobj):
+    """
+    A helper function to deal with replacements in files
+    repobj: A dictionary with "prev" and "to" keys
+    """
+    assert len(repobj["prev"]) == len(
+        repobj["to"]
+    ), "The replacement dictionary must contain as many targets as values"
+    with open(fname, "r") as f:
+        fInp = f.read()
+    for p, t in zip(repobj["prev"], repobj["to"]):
+        fInp = fInp.replace(p, t)
+    with open(fname, "w") as o:
+        o.write(fInp)
+
+
+class DotDict(dict):
+    """
+    Modified dictionary class for accessing key:val via dot notation.
+    Inspired by the MIT licensed (defunct) Konfik library
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        for key in self.keys():
+            if isinstance(self[key], dict):
+                self[key] = DotDict(self[key])
+
+    def __getitem__(self, key):
+        if isinstance(key, str):
+            try:
+                return super().__getitem__(key)
+            except KeyError:
+                raise MissingVariableError(f"No such variable '{key}' exists") from None
+        else:
+            raise TypeError("Key must be a string")
+
+    def __setitem__(self, key, value):
+        if isinstance(value, dict) and not isinstance(value, DotDict):
+            value = DotDict(value)
+        super().__setitem__(key, value)
+
+    def __getattr__(self, key):
+        if key.startswith("__") and key.endswith("__"):
+            return super().__getattr__(key)
+        return self.__getitem__(key)
+
+    def __setattr__(self, key, value):
+        if key.startswith("__") and key.endswith("__"):
+            super().__setattr__(key, value)
+        else:
+            self.__setitem__(key, value)
+
+    def __delattr__(self, key):
+        if key in self:
+            del self[key]
+        else:
+            super().__delattr__(key)
diff --git a/wailord/cli.py b/wailord/cli.py
index bb2b3ed..43d0f6b 100644
--- a/wailord/cli.py
+++ b/wailord/cli.py
@@ -6,12 +6,7 @@
 
 
 @click.command()
-# @click.option('--count', default=1, help='Number of greetings.')
-# @click.option('--conf', prompt='Input file',
-#               help='Configuration file in TOML, YAML, DOTENV or JSON')
-@click.option(
-    "--conf", default=None, help="Configuration file in TOML, YAML, DOTENV or JSON"
-)
+@click.option("--conf", default=None, help="Configuration file in YAML")
 @click.option(
     "--experiment",
     default="basicExperiment",
@@ -25,15 +20,3 @@ def main(conf, experiment):
 
 if __name__ == "__main__":
     sys.exit(main())  # pragma: no cover
-
-# @click.command()
-# @click.option('--count', default=1, help='Number of greetings.')
-# @click.option('--name', prompt='Your name',
-#               help='The person to greet.')
-# def hello(count, name):
-#     """Simple program that greets NAME for a total of COUNT times."""
-#     for x in range(count):
-#         click.echo('Hello %s!' % name)
-
-# if __name__ == '__main__':
-#     hello()
diff --git a/wailord/exp/cookies.py b/wailord/exp/cookies.py
index 44db9c5..e606a4d 100644
--- a/wailord/exp/cookies.py
+++ b/wailord/exp/cookies.py
@@ -3,31 +3,34 @@
 """
 from cookiecutter.main import cookiecutter
 from pathlib import Path
-from konfik import Konfik
+import yaml
 
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
-TEMPLATE_DIR = get_project_root() / "wailord_templates"
+TEMPLATE_DIR = get_project_root() / "wailord" / "_templates"
 
 
 def gen_base(filen=None, /, template="basicExperiment", *, absolute=False):
     """Generate a base template"""
-    if absolute == True:
+    if absolute:
         template = str(template)
     else:
         template = str(TEMPLATE_DIR / template)
+
     if filen is not None:
-        konfik = Konfik(config_path=filen)
-        config = konfik.config
-        if absolute is False:
-            config.orca_yml = Path(config.orca_yml).resolve()
-            config.inp_xyz = Path(config.inp_xyz).resolve()
+        with open(filen, "r") as ymlfile:
+            config = yaml.safe_load(ymlfile)
+
+        if not absolute:
+            config["orca_yml"] = str(Path(config["orca_yml"]).resolve())
+            config["inp_xyz"] = str(Path(config["inp_xyz"]).resolve())
+
         cookiecutter(
             template,
             no_input=True,
             overwrite_if_exists=True,
             extra_context=config,
-            output_dir=Path(config.outdir),
+            output_dir=Path(config["outdir"]),
         )
     else:
         # Create project from the basic template
diff --git a/wailord/io/inp.py b/wailord/io/inp.py
index c1b89da..76aa671 100644
--- a/wailord/io/inp.py
+++ b/wailord/io/inp.py
@@ -36,7 +36,7 @@
 
 """
 import wailord.io as waio
-import wailord.utils as wau
+import wailord._utils as wau
 
 import os
 import shutil
@@ -46,7 +46,7 @@
 from pathlib import Path
 from operator import itemgetter
 
-from konfik import Konfik
+import yaml
 
 SCAN_TYPES = {"D": "Dihedral", "B": "Bond", "A": "Angle"}
 CONSTRAINT_TYPES = {"D": "Dihedral", "B": "Bond", "A": "Angle", "C": "Cartesian"}
@@ -69,23 +69,25 @@ def __init__(self, filename):
         self.paramlines = None
         self.keylines = None
         self.blocks = None
-        self.konfik = Konfik(config_path=filename)
+        self.config = None
         self.scripts = []
 
+        fpath = Path(filename)
+        with fpath.open(mode="r") as ymlfile:
+            self.config = wau.DotDict(yaml.safe_load(ymlfile))
+
     def __repr__(self):
-        return f"{self.konfik.show_config()}"
+        return f"{self.config}"
 
     def read_yml(self):
-        """ Returns the overall output. """
-        self.qc, self.xyzpath, self.spin = itemgetter("qc", "xyz", "spin")(
-            self.konfik.config
-        )
+        """Returns the overall output."""
+        self.qc, self.xyzpath, self.spin = itemgetter("qc", "xyz", "spin")(self.config)
         # Test later
         if "basis_sets" not in self.qc:
             self.qc["basis_sets"] = ["semi_emp"]
         # Test this later, with and without, also try overrides
-        if "extra" in self.konfik.config.keys():
-            self.extra = self.konfik.config.extra
+        if "extra" in self.config:
+            self.extra = self.config["extra"]
         else:
             print("Consider using None in the yml file for extra")
 
@@ -190,24 +192,22 @@ def parse_xyz(self):
         """Generate folder structure for each system"""
         self.xyzpath = Path(self.xyzpath)
         if not self.xyzpath.is_dir():
-            self.xyz.append(
-                waio.xyz.xyzIO(self.conf_path.parent / self.konfik.config.xyz)
-            )
+            self.xyz.append(waio.xyz.xyzIO(self.conf_path.parent / self.config.xyz))
             self.xyzlines.append(self.xyz[-1].xyzdat.coord_block)
             # Geometry
-            if "geom" in self.konfik.config.keys():
-                self.geomlines = self.parse_geom(self.konfik.config.geom)
+            if "geom" in self.config:
+                self.geomlines = self.parse_geom(self.config.geom)
             # Paramter Blocks
-            if "params" in self.konfik.config.keys():
-                self.paramlines = self.parse_params(self.konfik.config.params)
-            if "scf" in self.konfik.config.keys():
-                self.scf = self.parse_scf(self.konfik.config.scf)
-            if "viz" in self.konfik.config.keys():
-                self.viz = self.parse_viz(self.konfik.config.viz)
-            if "keywords" in self.konfik.config.keys():
-                self.keylines = self.parse_keywords(self.konfik.config.keywords)
-            if "blocks" in self.konfik.config.keys():
-                self.blocks = self.parse_blocks(self.konfik.config.blocks)
+            if "params" in self.config:
+                self.paramlines = self.parse_params(self.config.params)
+            if "scf" in self.config:
+                self.scf = self.parse_scf(self.config.scf)
+            if "viz" in self.config:
+                self.viz = self.parse_viz(self.config.viz)
+            if "keywords" in self.config:
+                self.keylines = self.parse_keywords(self.config.keywords)
+            if "blocks" in self.config:
+                self.blocks = self.parse_blocks(self.config.blocks)
             self.gendir_qc(extra=None)
         else:
             for root, dirs, files in os.walk(self.xyzpath.resolve()):
@@ -218,23 +218,19 @@ def parse_xyz(self):
                         )
                         self.xyzlines.append(self.xyz[-1].xyzdat.coord_block)
                         # Geometry
-                        if "geom" in self.konfik.config.keys():
-                            self.geomlines = self.parse_geom(self.konfik.config.geom)
+                        if "geom" in self.config.keys():
+                            self.geomlines = self.parse_geom(self.config.geom)
                             # Paramter Blocks
-                        if "params" in self.konfik.config.keys():
-                            self.paramlines = self.parse_params(
-                                self.konfik.config.params
-                            )
-                        if "scf" in self.konfik.config.keys():
-                            self.scf = self.parse_scf(self.konfik.config.scf)
-                        if "viz" in self.konfik.config.keys():
-                            self.viz = self.parse_viz(self.konfik.config.viz)
-                        if "keywords" in self.konfik.config.keys():
-                            self.keylines = self.parse_keywords(
-                                self.konfik.config.keywords
-                            )
-                        if "blocks" in self.konfik.config.keys():
-                            self.blocks = self.parse_blocks(self.konfik.config.blocks)
+                        if "params" in self.config.keys():
+                            self.paramlines = self.parse_params(self.config.params)
+                        if "scf" in self.config.keys():
+                            self.scf = self.parse_scf(self.config.scf)
+                        if "viz" in self.config.keys():
+                            self.viz = self.parse_viz(self.config.viz)
+                        if "keywords" in self.config.keys():
+                            self.keylines = self.parse_keywords(self.config.keywords)
+                        if "blocks" in self.config.keys():
+                            self.blocks = self.parse_blocks(self.config.blocks)
                         self.gendir_qc(extra=None)
         pass
 
@@ -373,18 +369,24 @@ def genharness(self, basename, slow=False):
             op.write("#!/usr/bin/env bash\n")
             op.write("export cur_file=$(realpath $0) \n")
             op.write('export cur_dir=$(dirname "${cur_file}")\n')
+
+            # Define the job command based on the availability of qsub
+            op.write("if command -v qsub &> /dev/null; then\n")
+            op.write("    job_command=\"qsub\"\n")
+            op.write("else\n")
+            op.write("    echo \"qsub not found, using bash instead.\"\n")
+            op.write("    job_command=\"bash\"\n")
+            op.write("fi\n")
+            op.write("\n")
             for num, script in enumerate(self.scripts, start=1):
-                op.write(f'cd "./{script.parents[0]}"')
-                op.write("\n")
-                op.write(f"qsub './{script.name}'")
-                op.write("\n")
+                op.write(f'cd "./{script.parents[0]}"\n')
+                op.write(f"${{job_command}} './{script.name}'\n")
                 op.write("cd $cur_dir\n")
                 op.write("\n")
-                if slow is True:
-                    if num % 10 == 0:
-                        op.write('echo("Slowing down!")\n')
-                        op.write("sleep 30s\n")
-        pass
+                if slow is True and num % 10 == 0:
+                    op.write('echo "Slowing down!"\n')
+                    op.write("sleep 30s\n")
+                    op.write("\n")
 
     def parse_qc(self):
         qcList = list(
@@ -400,7 +402,7 @@ def gendir_qc(self, basename=None, extra=None):
         if extra is not None:
             print("Overwriting extra from yml file")
             self.extra = extra
-        for styl in self.konfik.config.qc.style:
+        for styl in self.config.qc.style:
             styl = styl.replace(" ", "_")
             self.gendir_qcspin(basename / styl)
         self.genharness(basename)
@@ -415,14 +417,14 @@ def gendir_qcspin(self, path):
 
     def gendir_qccalc(self, path):
         """Generates set of calculation folders"""
-        for cal in self.konfik.config.qc.calculations:
+        for cal in self.config.qc.calculations:
             self.gendir_qcbasis(path / cal)
         pass
 
     def gendir_qcbasis(self, path):
         """Generates the directory of input files. Note that the folders will have +
         replaced by P and * by 8"""
-        for base in self.konfik.config.qc.basis_sets:
+        for base in self.config.qc.basis_sets:
             bas = base.replace("+", "P").replace("*", "8")
             Path.mkdir(path / bas, parents=True, exist_ok=True)
             self.geninp(path / bas)
@@ -448,7 +450,7 @@ def geninp(self, path):
         self.writeinp(tmpconf)
         self.putscript(
             to_loc=path,
-            from_loc=self.conf_path.parent / self.konfik.config.jobscript,
+            from_loc=self.conf_path.parent / self.config.jobscript,
             slug=f"{tmpconf['basis']}_{tmpconf['style']}",
         )
         pass
@@ -456,7 +458,7 @@ def geninp(self, path):
     def putscript(self, from_loc, to_loc, slug):
         """Copies the jobscript"""
         shutil.copy(from_loc, to_loc)
-        scriptname = to_loc / self.konfik.config.jobscript
+        scriptname = to_loc / self.config.jobscript
         slug = slug.replace(" ", "_")
         rep_obj = {
             "prev": ["ORCA_CALCULATION"],
@@ -464,7 +466,7 @@ def putscript(self, from_loc, to_loc, slug):
         }
         wau.repkey(scriptname, rep_obj)
         if self.viz is not None:
-            if self.konfik.config.viz.chemcraft is True:
+            if self.config.viz.chemcraft is True:
                 with open(scriptname, "a") as script:
                     string = """
                     cd $SLURM_SUBMIT_DIR
@@ -513,7 +515,7 @@ def writeinp(self, confobj, extralines=None):
 
 
 class simpleInput:
-    """ Base class for representing the simple input line"""
+    """Base class for representing the simple input line"""
 
     def __init__(self, data):
         self.contents = None
diff --git a/wailord/io/orca.py b/wailord/io/orca.py
index 70c56d6..347b0ac 100644
--- a/wailord/io/orca.py
+++ b/wailord/io/orca.py
@@ -31,9 +31,6 @@
 
 """
 
-import wailord.io as waio
-import wailord.utils as wau
-
 import numpy as np
 import pandas as pd
 import itertools as itertt
@@ -51,7 +48,7 @@
 from collections import namedtuple, OrderedDict
 from operator import itemgetter
 from pandas.api.types import CategoricalDtype
-from konfik import Konfik
+import yaml
 
 # Pint setup
 PA_ = pint_pandas.PintArray
@@ -367,7 +364,9 @@ def handle_exp(self, efol):
 
         """
         fnames = []
-        self.inpconf = Konfik(config_path=efol / "orca.yml").config
+        orca_config_path = Path(efol) / "orca.yml"
+        with orca_config_path.open(mode="r") as ymlfile:
+            self.inpconf = yaml.safe_load(ymlfile)
         for root, dirs, files in os.walk(efol.resolve()):
             for filename in files:
                 if "out" in filename and "slurm" not in filename:
@@ -533,12 +532,12 @@ def get_population(self, poptype=["Mulliken", "Loewdin"], /):
         return popdat
 
     def visit_meta(self, node, visited_children):
-        """ Returns the overall output. """
+        """Returns the overall output."""
         self.meta = node.text
         return node.text
 
     def visit_coord_block(self, node, visited_children):
-        """ Makes a dict of the section (as key) and the key/value pairs. """
+        """Makes a dict of the section (as key) and the key/value pairs."""
         cb = node.text.split("\n")
         for i, aline in enumerate(cb):
             each = aline.split()
diff --git a/wailord/io/xyz.py b/wailord/io/xyz.py
index c236c63..fa09340 100644
--- a/wailord/io/xyz.py
+++ b/wailord/io/xyz.py
@@ -62,12 +62,12 @@ def __repr__(self):
         return f"{self.meta}"
 
     def visit_meta(self, node, visited_children):
-        """ Returns the overall output. """
+        """Returns the overall output."""
         self.meta = node.text
         return node.text
 
     def visit_coord_block(self, node, visited_children):
-        """ Makes a dict of the section (as key) and the key/value pairs. """
+        """Makes a dict of the section (as key) and the key/value pairs."""
         cb = node.text.split("\n")
         for i, aline in enumerate(cb):
             each = aline.split()
@@ -77,17 +77,17 @@ def visit_coord_block(self, node, visited_children):
         return node.text
 
     def visit_cline(self, node, visited_children):
-        """ Makes a dict of the section (as key) and the key/value pairs. """
+        """Makes a dict of the section (as key) and the key/value pairs."""
         self.clines = node.text
         return node.text
 
     def visit_natoms(self, node, visited_children):
-        """ Makes a dict of the section (as key) and the key/value pairs. """
+        """Makes a dict of the section (as key) and the key/value pairs."""
         print(node.text)
         return node.text
 
     def visit_atype(self, node, visited_children):
-        """ Makes a dict of the section (as key) and the key/value pairs. """
+        """Makes a dict of the section (as key) and the key/value pairs."""
         self.atom_types.append(node.text)
         return node.text
 
diff --git a/wailord/utils.py b/wailord/utils.py
deleted file mode 100644
index 13f251b..0000000
--- a/wailord/utils.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from pathlib import Path
-
-
-def get_project_root() -> Path:
-    """
-    A helper to obtain the project root path
-    From here: https://stackoverflow.com/a/53465812/1895378
-    """
-    return Path(__file__).parent.parent
-
-
-def repkey(fname, repobj):
-    """
-    A helper function to deal with replacements in files
-    repobj: A dictionary with "prev" and "to" keys
-    """
-    assert len(repobj["prev"]) == len(
-        repobj["to"]
-    ), "The replacement dictionary must contain as many targets as values"
-    with open(fname, "r") as f:
-        fInp = f.read()
-    for p, t in zip(repobj["prev"], repobj["to"]):
-        fInp = fInp.replace(p, t)
-    with open(fname, "w") as o:
-        o.write(fInp)
diff --git a/wailord/wailord.py b/wailord/wailord.py
deleted file mode 100644
index dd0b80e..0000000
--- a/wailord/wailord.py
+++ /dev/null
@@ -1,1 +0,0 @@
-"""Main module."""


Test patch:
diff --git a/tests/fakeCookie.py b/tests/fakeCookie.py
index b46a81a..b78c835 100644
--- a/tests/fakeCookie.py
+++ b/tests/fakeCookie.py
@@ -1,7 +1,7 @@
 import wailord.io as waio
 import wailord.exp as waex
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
 DATA_DIR = get_project_root() / "tests" / "data"
 
-waex.cookies.gen_base(filen=DATA_DIR / "cookieExp.yml")
+waex.cookies.gen_base(DATA_DIR / "cookieExp.yml")
diff --git a/tests/fakeIO.py b/tests/fakeIO.py
index 45772fc..aad1f7e 100644
--- a/tests/fakeIO.py
+++ b/tests/fakeIO.py
@@ -1,5 +1,5 @@
 import wailord.io as waio
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
 DATA_DIR = get_project_root() / "tests" / "data"
 
diff --git a/tests/fakeInp.py b/tests/fakeInp.py
index 733034b..74f3254 100644
--- a/tests/fakeInp.py
+++ b/tests/fakeInp.py
@@ -1,5 +1,5 @@
 import wailord.io as waio
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
 CONF_DIR = (
     get_project_root()
@@ -17,55 +17,3 @@
 ymlt = waio.inp.inpGenerator(DATA_DIR / "orcaGeom.yml")
 ymlt.parse_yml()
 ymlt.gendir_qc()
-
-# # Make this more general
-# sx = waio.xyz.xyzIO(DATA_DIR / "h2mol.xyz")
-# print(sx.comment_line)
-# sx.write("t.xyz")
-# from pathlib import Path
-# from konfik import Konfik
-# import itertools as itertt
-
-# # Define the config path
-# BASE_DIR = Path(__file__).parent
-# CONFIG_PATH_YML = BASE_DIR / "../templates/baseAssignment/orca.yml"
-
-# # Initialize the konfik class
-# konfik = Konfik(config_path=CONFIG_PATH_YML)
-
-# # Print the config file as a Python dict
-# konfik.show_config()
-
-# # Get the config dict from the konfik class
-# config = konfik.config
-
-# # Handle the config dictionary
-# while True:
-#     try:
-#         print(f"Dictionary length: {len(config)}")
-#         item = config.popitem()
-#         # Do something with item here...
-#         print(f"{item} removed")
-#     except KeyError:
-#         print("The dictionary has no item now...")
-#         break
-
-# for key in config:
-#     print(key)
-
-# # possibleConf = [
-# #     j for i in itertt.zip_longest(config.qc.calculations, config.basis_sets) for j in i
-# # ]
-
-# # for conf in itertt.product(possibleConf):
-# #     print(f"{conf} from {len(config.basis_sets)}")
-
-
-# def genInp(config):
-#     pass
-#     return
-
-
-# def countConf(config):
-#     pass
-#     return numConf
diff --git a/tests/fakeOrca.py b/tests/fakeOrca.py
index f0ef1a3..8547529 100644
--- a/tests/fakeOrca.py
+++ b/tests/fakeOrca.py
@@ -1,17 +1,6 @@
 import wailord.io as waio
-from wailord.utils import get_project_root
+from wailord._utils import get_project_root
 
 DATA_DIR = get_project_root() / "tests"
 
-# sorc = waio.orca.orcaIO(DATA_DIR / "orca_opt.out")
-# sEnerg = waio.orca.genEBASet(DATA_DIR / "h2")
-# print(sEnerg)
-# print(sEnerg.sort_values(by=["basis"], ascending=False, ignore_index=True))
-
-# sEnerg = waio.orca.orcaVis(
-#     ofile=DATA_DIR / "io/test_io" / "h2/h_h_mol/QCISD(T)/spin_01/ENERGY/3-21G/orca.out"
-# )
-# print(sEnerg.mult_energy_surface())
-
 expt = waio.orca.orcaExp(expfolder=DATA_DIR / "io/test_io" / "h2")
-# edat = expt.get_energy_surface(etype=["MDCI", "Actual Energy"])
diff --git a/tests/io/orca/singles/test_sp.py b/tests/io/orca/singles/test_sp.py
index 311e79e..1dc026b 100644
--- a/tests/io/orca/singles/test_sp.py
+++ b/tests/io/orca/singles/test_sp.py
@@ -4,7 +4,8 @@
 import warnings
 import pytest
 
-from siuba import _, filter, select, mutate
+import siuba as si
+from siuba import _
 
 from pint import UnitRegistry
 from pathlib import Path
@@ -264,8 +265,8 @@ def test_orca_nstep_pop(datadir):
     spop = waio.orca.orcaVis(ofile=datadir / "ch3f_3ang_b3lyp.out")
     popdat = spop.single_population_analysis()
     assert popdat.step.max() == 2
-    assert (popdat >> filter(_.step == 1)).shape == (
-        popdat >> filter(_.step == 2)
+    assert (popdat >> si.filter(_.step == 1)).shape == (
+        popdat >> si.filter(_.step == 2)
     ).shape
     pass
 
diff --git a/tests/io/orca/test_io.py b/tests/io/orca/test_io.py
index fbd405f..520771f 100644
--- a/tests/io/orca/test_io.py
+++ b/tests/io/orca/test_io.py
@@ -4,7 +4,8 @@
 import pytest
 
 from pint import UnitRegistry
-from siuba import _, filter, select, mutate
+import siuba as si
+from siuba import _
 
 ureg = UnitRegistry()
 Q_ = ureg.Quantity
@@ -205,7 +206,7 @@ def test_get_ir_freq(datadir):
     expt = waio.orca.orcaExp(expfolder=datadir / "ir_spec", order_theory=oth)
     vdat = expt.get_ir_spec()
     assert vdat.shape == (63, 11)
-    assert (vdat >> filter(_.slug == "O1H2_h2o")).shape == (9, 11)
+    assert (vdat >> si.filter(_.slug == "O1H2_h2o")).shape == (9, 11)
     pass
 
 
diff --git a/tests/test_wailord.py b/tests/test_wailord.py
deleted file mode 100644
index 5acc64c..0000000
--- a/tests/test_wailord.py
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/usr/bin/env python
-
-"""Tests for `wailord` package."""
-
-import pytest
-
-from click.testing import CliRunner
-
-from wailord import wailord
-from wailord import cli
-
-from wailord.utils import get_project_root
-
-# DATA_DIR = get_project_root() / "tests" / "data"
-
-# @pytest.fixture
-# def response():
-#     """Sample pytest fixture.
-
-#     See more at: http://doc.pytest.org/en/latest/fixture.html
-#     """
-#     # import requests
-#     # return requests.get('https://github.com/audreyr/cookiecutter-pypackage')
-
-
-# def test_content(response):
-#     """Sample pytest test function with the pytest fixture as an argument."""
-#     # from bs4 import BeautifulSoup
-#     # assert 'GitHub' in BeautifulSoup(response.content).title.string
-
-
-# def test_command_line_interface():
-#     """Test the CLI."""
-#     runner = CliRunner()
-#     result = runner.invoke(cli.main(args="--name={DATA_DIR}/trial.yml"))
-#     assert result.exit_code == 0
-#     assert 'wailord.cli.main' in result.output
-#     help_result = runner.invoke(cli.main, ['--help'])
-#     assert help_result.exit_code == 0
-#     assert '--help  Show this message and exit.' in help_result.output