Repository: DiamondLightSource/httomo (language: python)

Issue:
Inconsistent placement of `*_modules.yaml` file needed for YAML template generation
Backends have their `*_modules.yaml` file in `httomo/methods_database/`, ie:
- httomolib: https://github.com/DiamondLightSource/httomo/tree/4429711ab89ed1efe86d9c3be260df25fc7f1999/httomo/methods_database/packages/external/httomolib
- httomolibgpu: https://github.com/DiamondLightSource/httomo/tree/4429711ab89ed1efe86d9c3be260df25fc7f1999/httomo/methods_database/packages/external/httomolibgpu
- tomopy: https://github.com/DiamondLightSource/httomo/tree/4429711ab89ed1efe86d9c3be260df25fc7f1999/httomo/methods_database/packages/external/tomopy

However, the `httomo_modules.yaml` (needed to generate YAML templates) is in the `yaml_templates/` dir itself: https://github.com/DiamondLightSource/httomo/blob/4429711ab89ed1efe86d9c3be260df25fc7f1999/httomo/yaml_templates/httomo/httomo_modules.yaml

Given that `httomo_modules.yaml` will be needed to autogenerate httomo YAML templates that _go into_ `yaml_templates/`, it would be sensible to move this file out of `yaml_templates/` and into `httomo/methods_database/packages`


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/doc_conda.yml b/.github/workflows/doc_conda.yml
index 98f45c857..40c05ebea 100644
--- a/.github/workflows/doc_conda.yml
+++ b/.github/workflows/doc_conda.yml
@@ -36,10 +36,10 @@ jobs:
 
         - name: Generate yaml templates
           run: |
-            python ./httomo/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/tomopy/tomopy_modules.yaml -o ./docs/build/yaml_templates/tomopy
-            python ./httomo/yaml_unsupported_tomopy_remove.py -t ./docs/build/yaml_templates/tomopy -l ./httomo/methods_database/packages/external/tomopy/tomopy.yaml
-            python ./httomo/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/httomolib/httomolib_modules.yaml -o ./docs/build/yaml_templates/httomolib
-            python ./httomo/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/httomolibgpu/httomolibgpu_modules.yaml -o ./docs/build/yaml_templates/httomolibgpu
+            python ./scripts/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/tomopy/tomopy_modules.yaml -o ./docs/build/yaml_templates/tomopy
+            python ./scripts/yaml_unsupported_tomopy_remove.py -t ./docs/build/yaml_templates/tomopy -l ./httomo/methods_database/packages/external/tomopy/tomopy.yaml
+            python ./scripts/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/httomolib/httomolib_modules.yaml -o ./docs/build/yaml_templates/httomolib
+            python ./scripts/yaml_templates_generator.py -i ./httomo/methods_database/packages/external/httomolibgpu/httomolibgpu_modules.yaml -o ./docs/build/yaml_templates/httomolibgpu
 
         - name: Generate yml docs
           run: python ./docs/source/yaml_doc_generator.py
diff --git a/conda/recipe/build.sh b/conda/recipe/build.sh
index bdfbf848a..76f9d82ac 100755
--- a/conda/recipe/build.sh
+++ b/conda/recipe/build.sh
@@ -1,3 +1,23 @@
 #!/bin/bash
 
 python -m pip install .
+
+# Define var for path to httomo installation dir
+#
+# `SP_DIR` is the path to the `site-packages/` dir in the conda env, see
+# https://docs.conda.io/projects/conda-build/en/latest/user-guide/environment-variables.html#environment-variables-set-during-the-build-process
+HTTOMO_TARGET="$SP_DIR/$PKG_NAME"
+
+# Create dirs for YAML templates
+mkdir $HTTOMO_TARGET/yaml_templates/
+mkdir $HTTOMO_TARGET/yaml_templates/httomo
+mkdir $HTTOMO_TARGET/yaml_templates/httomolib
+mkdir $HTTOMO_TARGET/yaml_templates/httomolibgpu
+mkdir $HTTOMO_TARGET/yaml_templates/tomopy
+
+# Generate YAML templates
+python scripts/yaml_templates_generator.py -i httomo/methods_database/packages/httomo_modules.yaml -o $HTTOMO_TARGET/yaml_templates/httomo/
+python scripts/yaml_templates_generator.py -i httomo/methods_database/packages/external/httomolib/httomolib_modules.yaml -o $HTTOMO_TARGET/yaml_templates/httomolib/
+python scripts/yaml_templates_generator.py -i httomo/methods_database/packages/external/httomolibgpu/httomolibgpu_modules.yaml -o $HTTOMO_TARGET/yaml_templates/httomolibgpu/
+python scripts/yaml_templates_generator.py -i httomo/methods_database/packages/external/tomopy/tomopy_modules.yaml -o $HTTOMO_TARGET/yaml_templates/tomopy/
+python scripts/yaml_unsupported_tomopy_remove.py -t $HTTOMO_TARGET/yaml_templates/tomopy/ -l httomo/methods_database/packages/external/tomopy/tomopy.yaml
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index e0af9c06f..08f6b9b37 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -29,25 +29,43 @@ test:
     - pip check
     - pytest 
 requirements:
-  host:
-    - python
+  build:
+    - h5py=*=*mpi_openmpi*
+    - httomolib==2.0
+    - httomolibgpu==2.0
+    - loguru
+    - mpi4py
+    - numpy<=1.25
     - pip
+    - python
+    - pyyaml
     - setuptools
     - setuptools-git-versioning
+    - tomopy==1.15
+    - typing_extensions
   run:
-    - python
-    - numpy>= 1.20, <= 1.25
-    - cupy>=12.3
-    - mpi4py>=3.1
-    - h5py>=3.8=mpi*
-    - httomolib
-    - tomopy
+    - astra-toolbox
+    - click>=8.1.3
+    - cucim
+    - cupy<=12.3.0
+    - cudatoolkit
+    - graypy
+    - h5py=*=*mpi_openmpi*
+    - hdf5plugin
+    - httomolib==2.0
+    - httomolibgpu==2.0
+    - ipython
+    - loguru
+    - mpi4py
     - pyyaml
+    - numpy<=1.25
     - nvtx
-    - click
-    - setuptools
-    - pytest
+    - python
     - plumbum
+    - tomobar
+    - tomopy==1.15
+    - tqdm
+    - typing_extensions
 
 about:
   home: https://github.com/DiamondLightSource/httomo
diff --git a/conda/recipe/samples b/conda/recipe/samples
deleted file mode 120000
index 0a9c8f867..000000000
--- a/conda/recipe/samples
+++ /dev/null
@@ -1,1 +0,0 @@
-../../tests/samples/
\ No newline at end of file
diff --git a/conda/recipe/yaml_templates b/conda/recipe/yaml_templates
deleted file mode 120000
index 24a0198ed..000000000
--- a/conda/recipe/yaml_templates
+++ /dev/null
@@ -1,1 +0,0 @@
-../../yaml_templates/
\ No newline at end of file
diff --git a/docs/source/howto/installation.rst b/docs/source/howto/installation.rst
index 51977e636..9593866c4 100644
--- a/docs/source/howto/installation.rst
+++ b/docs/source/howto/installation.rst
@@ -34,4 +34,4 @@ Build HTTomo as a conda Python package
 ======================================================
 .. code-block:: console
 
-   $ conda build conda/recipe/ -c conda-forge -c https://conda.anaconda.org/httomo/ 
+   $ conda build conda/recipe/ -c conda-forge -c https://conda.anaconda.org/httomo/ -c rapidsai
diff --git a/docs/source/utilities/yaml_generator.rst b/docs/source/utilities/yaml_generator.rst
index f0adeb10f..7e5e98e48 100644
--- a/docs/source/utilities/yaml_generator.rst
+++ b/docs/source/utilities/yaml_generator.rst
@@ -2,7 +2,7 @@
 
 Templates generator
 *******************
-:ref:`backends_content` can be generated automatically using the YAML generator tool `provided <https://github.com/DiamondLightSource/httomo/tree/main/httomo/yaml_templates_generator.py>`_ in the Github repo. 
+:ref:`backends_content` can be generated automatically using the YAML generator tool `provided <https://github.com/DiamondLightSource/httomo/tree/main/scripts/yaml_templates_generator.py>`_ in the Github repo. 
 
 The script does the following: 
 
@@ -30,4 +30,4 @@ Please note that the package from which the modules are extracted, must be insta
  
 .. code-block:: console
    
-   $ python -m remove_unsupported_templates -t /path/to/templates/ -l /path/to/library/file
\ No newline at end of file
+   $ python -m remove_unsupported_templates -t /path/to/templates/ -l /path/to/library/file
diff --git a/httomo/yaml_templates/httomo/httomo_modules.yaml b/httomo/methods_database/packages/httomo_modules.yaml
similarity index 100%
rename from httomo/yaml_templates/httomo/httomo_modules.yaml
rename to httomo/methods_database/packages/httomo_modules.yaml
diff --git a/httomo/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml b/httomo/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml
deleted file mode 100644
index 893e1b423..000000000
--- a/httomo/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-- method: standard_tomo
-  module_path: httomo.data.hdf.loaders
-  parameters:
-    name: REQUIRED
-    data_path: REQUIRED
-    dimension: REQUIRED
-    preview: REQUIRED
-    pad: REQUIRED
-    image_key_path: null
-    rotation_angles:
-      data_path: /entry1/tomo_entry/data/rotation_angle
-    ignore_darks: false
-    ignore_flats: false
diff --git a/httomo/yaml_templates/httomo/httomo.methods/calculate_stats.yaml b/httomo/yaml_templates/httomo/httomo.methods/calculate_stats.yaml
deleted file mode 100644
index b865f53b1..000000000
--- a/httomo/yaml_templates/httomo/httomo.methods/calculate_stats.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: calculate_stats
-  module_path: httomo.methods
-  parameters: {}
-  id: statistics
-  side_outputs:
-    glob_stats: glob_stats
diff --git a/httomo/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml b/httomo/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml
deleted file mode 100644
index d26cb3d30..000000000
--- a/httomo/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-- method: save_to_images
-  module_path: httomolib.misc.images
-  parameters:
-    subfolder_name: images
-    axis: auto
-    file_format: tif
-    bits: 8
-    perc_range_min: 0.0
-    perc_range_max: 100.0
-    jpeg_quality: 95
-    glob_stats: ${{statistics.side_outputs.glob_stats}}
-    offset: 0
-    asynchronous: true
diff --git a/httomo/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml b/httomo/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml
deleted file mode 100644
index 293e8b255..000000000
--- a/httomo/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: data_reducer
-  module_path: httomolib.misc.morph
-  parameters:
-    axis: auto
-    method: mean
diff --git a/httomo/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml b/httomo/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml
deleted file mode 100644
index 0debaf0b0..000000000
--- a/httomo/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: binary_thresholding
-  module_path: httomolib.misc.segm
-  parameters:
-    val_intensity: 0.1
-    otsu: false
-    foreground: true
-    axis: auto
diff --git a/httomo/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml b/httomo/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
deleted file mode 100644
index 63da87de0..000000000
--- a/httomo/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: paganin_filter
-  module_path: httomolib.prep.phase
-  parameters:
-    pixel_size: 0.0001
-    dist: 50.0
-    energy: 53.0
-    alpha: 0.001
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml
deleted file mode 100644
index 9b7c3bdd5..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: median_filter
-  module_path: httomolibgpu.misc.corr
-  parameters:
-    kernel_size: 3
-    axis: auto
-    dif: 0.0
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml
deleted file mode 100644
index e7647420d..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: remove_outlier
-  module_path: httomolibgpu.misc.corr
-  parameters:
-    kernel_size: 3
-    axis: auto
-    dif: 0.1
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml
deleted file mode 100644
index 8c22a27eb..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: data_resampler
-  module_path: httomolibgpu.misc.morph
-  parameters:
-    newshape: REQUIRED
-    axis: auto
-    interpolation: linear
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml
deleted file mode 100644
index 8434e052f..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: sino_360_to_180
-  module_path: httomolibgpu.misc.morph
-  parameters:
-    overlap: ${{centering.side_outputs.overlap}}
-    rotation: left
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml
deleted file mode 100644
index bbea1017d..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: rescale_to_int
-  module_path: httomolibgpu.misc.rescale
-  parameters:
-    perc_range_min: 0.0
-    perc_range_max: 100.0
-    bits: 8
-    glob_stats: ${{statistics.side_outputs.glob_stats}}
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml
deleted file mode 100644
index 5e31d25e1..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: distortion_correction_proj_discorpy
-  module_path: httomolibgpu.prep.alignment
-  parameters:
-    metadata_path: REQUIRED
-    preview: REQUIRED
-    order: 1
-    mode: reflect
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml
deleted file mode 100644
index fae8feb4a..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: normalize
-  module_path: httomolibgpu.prep.normalize
-  parameters:
-    cutoff: 10.0
-    minus_log: true
-    nonnegativity: false
-    remove_nans: false
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml
deleted file mode 100644
index 1d7a5027a..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-- method: paganin_filter_savu
-  module_path: httomolibgpu.prep.phase
-  parameters:
-    ratio: 250.0
-    energy: 53.0
-    distance: 1.0
-    resolution: 1.28
-    pad_y: 100
-    pad_x: 100
-    pad_method: edge
-    increment: 0.0
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml
deleted file mode 100644
index 7752f1e7f..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: paganin_filter_tomopy
-  module_path: httomolibgpu.prep.phase
-  parameters:
-    pixel_size: 0.0001
-    dist: 50.0
-    energy: 53.0
-    alpha: 0.001
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
deleted file mode 100644
index 5cfa82c1e..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_all_stripe
-  module_path: httomolibgpu.prep.stripe
-  parameters:
-    snr: 3.0
-    la_size: 61
-    sm_size: 21
-    dim: 1
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml
deleted file mode 100644
index a113f74f8..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: remove_stripe_based_sorting
-  module_path: httomolibgpu.prep.stripe
-  parameters:
-    size: 11
-    dim: 1
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml
deleted file mode 100644
index 71332c0dc..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: remove_stripe_ti
-  module_path: httomolibgpu.prep.stripe
-  parameters:
-    beta: 0.1
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS.yaml
deleted file mode 100644
index b87272e6b..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: CGLS
-  module_path: httomolibgpu.recon.algorithm
-  parameters:
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    recon_size: null
-    iterations: 20
-    nonnegativity: true
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP.yaml
deleted file mode 100644
index 6a578b0dc..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: FBP
-  module_path: httomolibgpu.recon.algorithm
-  parameters:
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    filter_freq_cutoff: 0.6
-    recon_size: null
-    recon_mask_radius: null
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT.yaml
deleted file mode 100644
index ada743094..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: SIRT
-  module_path: httomolibgpu.recon.algorithm
-  parameters:
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    recon_size: null
-    iterations: 300
-    nonnegativity: true
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml
deleted file mode 100644
index 59435bf2f..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-- method: find_center_360
-  module_path: httomolibgpu.recon.rotation
-  parameters:
-    ind: null
-    win_width: 10
-    side: null
-    denoise: true
-    norm: false
-    use_overlap: false
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
-    overlap: overlap
-    side: side
-    overlap_position: overlap_position
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml
deleted file mode 100644
index 6777dea22..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-- method: find_center_pc
-  module_path: httomolibgpu.recon.rotation
-  parameters:
-    proj1: auto
-    proj2: auto
-    tol: 0.5
-    rotc_guess: null
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
diff --git a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml b/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml
deleted file mode 100644
index fc5739790..000000000
--- a/httomo/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-- method: find_center_vo
-  module_path: httomolibgpu.recon.rotation
-  parameters:
-    ind: null
-    smin: -50
-    smax: 50
-    srad: 6.0
-    step: 0.25
-    ratio: 0.5
-    drop: 20
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml
deleted file mode 100644
index f02934fbc..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: adjust_range
-  module_path: tomopy.misc.corr
-  parameters:
-    dmin: null
-    dmax: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml
deleted file mode 100644
index 401836769..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: circ_mask
-  module_path: tomopy.misc.corr
-  parameters:
-    axis: REQUIRED
-    ratio: 1
-    val: 0.0
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/download_all.yaml
deleted file mode 100644
index 64f4faecf..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/download_all.yaml
+++ /dev/null
@@ -1,72 +0,0 @@
-- method: sobel_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    axis: auto
-- method: remove_outlier1d
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
-    axis: auto
-- method: circ_mask
-  module_path: tomopy.misc.corr
-  parameters:
-    axis: REQUIRED
-    ratio: 1
-    val: 0.0
-- method: remove_outlier
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
-    axis: auto
-- method: median_filter3d
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
-- method: median_filter_nonfinite
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
-    callback: null
-- method: remove_ring
-  module_path: tomopy.misc.corr
-  parameters:
-    rec: REQUIRED
-    center_x: null
-    center_y: null
-    thresh: 300.0
-    thresh_max: 300.0
-    thresh_min: -100.0
-    theta_min: 30
-    rwidth: 30
-    int_mode: WRAP
-- method: remove_nan
-  module_path: tomopy.misc.corr
-  parameters:
-    val: 0.0
-- method: adjust_range
-  module_path: tomopy.misc.corr
-  parameters:
-    dmin: null
-    dmax: null
-- method: median_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
-    axis: auto
-- method: remove_neg
-  module_path: tomopy.misc.corr
-  parameters:
-    val: 0.0
-- method: gaussian_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    sigma: 3
-    order: 0
-    axis: auto
-- method: remove_outlier3d
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml
deleted file mode 100644
index 7e5baed7d..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: gaussian_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    sigma: 3
-    order: 0
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml
deleted file mode 100644
index 25a00a3ba..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: median_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml
deleted file mode 100644
index a469bac13..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: median_filter3d
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml
deleted file mode 100644
index 6afcf75f6..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: median_filter_nonfinite
-  module_path: tomopy.misc.corr
-  parameters:
-    size: 3
-    callback: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml
deleted file mode 100644
index ed802d399..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: remove_nan
-  module_path: tomopy.misc.corr
-  parameters:
-    val: 0.0
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml
deleted file mode 100644
index 10fb6d5b6..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: remove_neg
-  module_path: tomopy.misc.corr
-  parameters:
-    val: 0.0
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml
deleted file mode 100644
index 505534a4b..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: remove_outlier
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml
deleted file mode 100644
index f99d31a9b..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: remove_outlier1d
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml
deleted file mode 100644
index 4123734fd..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: remove_outlier3d
-  module_path: tomopy.misc.corr
-  parameters:
-    dif: REQUIRED
-    size: 3
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml
deleted file mode 100644
index 107c63552..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml
+++ /dev/null
@@ -1,12 +0,0 @@
-- method: remove_ring
-  module_path: tomopy.misc.corr
-  parameters:
-    rec: REQUIRED
-    center_x: null
-    center_y: null
-    thresh: 300.0
-    thresh_max: 300.0
-    thresh_min: -100.0
-    theta_min: 30
-    rwidth: 30
-    int_mode: WRAP
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml
deleted file mode 100644
index 4c0b30229..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: sobel_filter
-  module_path: tomopy.misc.corr
-  parameters:
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/download_all.yaml
deleted file mode 100644
index 7b195e51f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/download_all.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-- method: downsample
-  module_path: tomopy.misc.morph
-  parameters:
-    level: 1
-    axis: auto
-- method: trim_sinogram
-  module_path: tomopy.misc.morph
-  parameters:
-    center: REQUIRED
-    x: REQUIRED
-    y: REQUIRED
-    diameter: REQUIRED
-- method: upsample
-  module_path: tomopy.misc.morph
-  parameters:
-    level: 1
-    axis: auto
-- method: sino_360_to_180
-  module_path: tomopy.misc.morph
-  parameters:
-    overlap: ${{centering.side_outputs.overlap}}
-    rotation: left
-- method: pad
-  module_path: tomopy.misc.morph
-  parameters:
-    axis: REQUIRED
-    npad: null
-    mode: constant
-    '#additional parameters': AVAILABLE
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml
deleted file mode 100644
index 6a2e01519..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: downsample
-  module_path: tomopy.misc.morph
-  parameters:
-    level: 1
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml
deleted file mode 100644
index 44572c480..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: pad
-  module_path: tomopy.misc.morph
-  parameters:
-    axis: REQUIRED
-    npad: null
-    mode: constant
-    '#additional parameters': AVAILABLE
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml
deleted file mode 100644
index b7d1c0de7..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: sino_360_to_180
-  module_path: tomopy.misc.morph
-  parameters:
-    overlap: ${{centering.side_outputs.overlap}}
-    rotation: left
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml
deleted file mode 100644
index f020e2ec3..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: trim_sinogram
-  module_path: tomopy.misc.morph
-  parameters:
-    center: REQUIRED
-    x: REQUIRED
-    y: REQUIRED
-    diameter: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml b/httomo/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml
deleted file mode 100644
index 4168ba54a..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: upsample
-  module_path: tomopy.misc.morph
-  parameters:
-    level: 1
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml
deleted file mode 100644
index f7b9821e6..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: add_jitter
-  module_path: tomopy.prep.alignment
-  parameters:
-    low: 0
-    high: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml
deleted file mode 100644
index 350e13c9f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: add_noise
-  module_path: tomopy.prep.alignment
-  parameters:
-    ratio: 0.05
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml
deleted file mode 100644
index 35d8f51f4..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-- method: align_joint
-  module_path: tomopy.prep.alignment
-  parameters:
-    fdir: ./
-    iters: 10
-    pad: !!python/tuple
-    - 0
-    - 0
-    blur: true
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    algorithm: sirt
-    upsample_factor: 10
-    rin: 0.5
-    rout: 0.8
-    save: false
-    debug: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml
deleted file mode 100644
index 8c4d11c8c..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-- method: align_seq
-  module_path: tomopy.prep.alignment
-  parameters:
-    fdir: .
-    iters: 10
-    pad: !!python/tuple
-    - 0
-    - 0
-    blur: true
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    algorithm: sirt
-    upsample_factor: 10
-    rin: 0.5
-    rout: 0.8
-    save: false
-    debug: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml
deleted file mode 100644
index 57b2ace2b..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: blur_edges
-  module_path: tomopy.prep.alignment
-  parameters:
-    low: 0
-    high: 0.8
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml
deleted file mode 100644
index 6dec583e4..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: distortion_correction_proj
-  module_path: tomopy.prep.alignment
-  parameters:
-    xcenter: REQUIRED
-    ycenter: REQUIRED
-    list_fact: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml
deleted file mode 100644
index d8a4ae49f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: distortion_correction_sino
-  module_path: tomopy.prep.alignment
-  parameters:
-    ind: REQUIRED
-    xcenter: REQUIRED
-    ycenter: REQUIRED
-    list_fact: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/download_all.yaml
deleted file mode 100644
index 92efac69a..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/download_all.yaml
+++ /dev/null
@@ -1,67 +0,0 @@
-- method: add_noise
-  module_path: tomopy.prep.alignment
-  parameters:
-    ratio: 0.05
-- method: align_seq
-  module_path: tomopy.prep.alignment
-  parameters:
-    fdir: .
-    iters: 10
-    pad: !!python/tuple
-    - 0
-    - 0
-    blur: true
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    algorithm: sirt
-    upsample_factor: 10
-    rin: 0.5
-    rout: 0.8
-    save: false
-    debug: true
-- method: scale
-  module_path: tomopy.prep.alignment
-  parameters: {}
-- method: distortion_correction_sino
-  module_path: tomopy.prep.alignment
-  parameters:
-    ind: REQUIRED
-    xcenter: REQUIRED
-    ycenter: REQUIRED
-    list_fact: REQUIRED
-- method: shift_images
-  module_path: tomopy.prep.alignment
-  parameters:
-    sx: REQUIRED
-    sy: REQUIRED
-- method: align_joint
-  module_path: tomopy.prep.alignment
-  parameters:
-    fdir: ./
-    iters: 10
-    pad: !!python/tuple
-    - 0
-    - 0
-    blur: true
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    algorithm: sirt
-    upsample_factor: 10
-    rin: 0.5
-    rout: 0.8
-    save: false
-    debug: true
-- method: add_jitter
-  module_path: tomopy.prep.alignment
-  parameters:
-    low: 0
-    high: 1
-- method: blur_edges
-  module_path: tomopy.prep.alignment
-  parameters:
-    low: 0
-    high: 0.8
-- method: distortion_correction_proj
-  module_path: tomopy.prep.alignment
-  parameters:
-    xcenter: REQUIRED
-    ycenter: REQUIRED
-    list_fact: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml
deleted file mode 100644
index 7a628485b..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-- method: scale
-  module_path: tomopy.prep.alignment
-  parameters: {}
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml
deleted file mode 100644
index 8ed8fc2f6..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: shift_images
-  module_path: tomopy.prep.alignment
-  parameters:
-    sx: REQUIRED
-    sy: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/download_all.yaml
deleted file mode 100644
index ff76db5c0..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/download_all.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-- method: normalize_roi
-  module_path: tomopy.prep.normalize
-  parameters:
-    roi:
-    - 0
-    - 0
-    - 10
-    - 10
-- method: normalize_bg
-  module_path: tomopy.prep.normalize
-  parameters:
-    air: 1
-- method: normalize_nf
-  module_path: tomopy.prep.normalize
-  parameters:
-    flat_loc: REQUIRED
-    cutoff: null
-    averaging: mean
-- method: minus_log
-  module_path: tomopy.prep.normalize
-  parameters: {}
-- method: normalize
-  module_path: tomopy.prep.normalize
-  parameters:
-    cutoff: null
-    averaging: mean
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml
deleted file mode 100644
index 6d9558919..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-- method: minus_log
-  module_path: tomopy.prep.normalize
-  parameters: {}
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml
deleted file mode 100644
index f917f4f94..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: normalize
-  module_path: tomopy.prep.normalize
-  parameters:
-    cutoff: null
-    averaging: mean
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml
deleted file mode 100644
index 28088716e..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: normalize_bg
-  module_path: tomopy.prep.normalize
-  parameters:
-    air: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml
deleted file mode 100644
index 987749f86..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: normalize_nf
-  module_path: tomopy.prep.normalize
-  parameters:
-    flat_loc: REQUIRED
-    cutoff: null
-    averaging: mean
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml
deleted file mode 100644
index eae28603c..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-- method: normalize_roi
-  module_path: tomopy.prep.normalize
-  parameters:
-    roi:
-    - 0
-    - 0
-    - 10
-    - 10
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml
deleted file mode 100644
index e020a75b7..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-- method: retrieve_phase
-  module_path: tomopy.prep.phase
-  parameters:
-    pixel_size: 0.0001
-    dist: 50
-    energy: 20
-    alpha: 0.001
-    pad: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/download_all.yaml
deleted file mode 100644
index e508b8067..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/download_all.yaml
+++ /dev/null
@@ -1,75 +0,0 @@
-- method: remove_stripe_sf
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: 5
-- method: stripes_mask3d
-  module_path: tomopy.prep.stripe
-  parameters:
-    weights: REQUIRED
-    threshold: 0.6
-    min_stripe_length: 20
-    min_stripe_depth: 10
-    min_stripe_width: 5
-    sensitivity_perc: 85.0
-- method: remove_stripe_based_sorting
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: null
-    dim: 1
-- method: stripes_detect3d
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: 10
-    radius: 3
-- method: remove_stripe_fw
-  module_path: tomopy.prep.stripe
-  parameters:
-    level: null
-    wname: db5
-    sigma: 2
-    pad: true
-- method: remove_stripe_ti
-  module_path: tomopy.prep.stripe
-  parameters:
-    nblock: 0
-    alpha: 1.5
-- method: remove_dead_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 51
-    norm: true
-- method: remove_stripe_based_filtering
-  module_path: tomopy.prep.stripe
-  parameters:
-    sigma: 3
-    size: null
-    dim: 1
-- method: remove_large_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 51
-    drop_ratio: 0.1
-    norm: true
-- method: remove_stripe_based_fitting
-  module_path: tomopy.prep.stripe
-  parameters:
-    order: 3
-    sigma: !!python/tuple
-    - 5
-    - 20
-- method: remove_stripe_based_interpolation
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 31
-    drop_ratio: 0.1
-    norm: true
-- method: remove_all_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    la_size: 61
-    sm_size: 21
-    dim: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml
deleted file mode 100644
index 19c77f31d..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_all_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    la_size: 61
-    sm_size: 21
-    dim: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml
deleted file mode 100644
index 18dce1f5d..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: remove_dead_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 51
-    norm: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml
deleted file mode 100644
index ca24d3a0a..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_large_stripe
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 51
-    drop_ratio: 0.1
-    norm: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml
deleted file mode 100644
index ee584fb6f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: remove_stripe_based_filtering
-  module_path: tomopy.prep.stripe
-  parameters:
-    sigma: 3
-    size: null
-    dim: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml
deleted file mode 100644
index 9dc35b7a3..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_stripe_based_fitting
-  module_path: tomopy.prep.stripe
-  parameters:
-    order: 3
-    sigma: !!python/tuple
-    - 5
-    - 20
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml
deleted file mode 100644
index 29f7a6c59..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_stripe_based_interpolation
-  module_path: tomopy.prep.stripe
-  parameters:
-    snr: 3
-    size: 31
-    drop_ratio: 0.1
-    norm: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml
deleted file mode 100644
index f5f8d799a..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: remove_stripe_based_sorting
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: null
-    dim: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml
deleted file mode 100644
index 5aa654390..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: remove_stripe_fw
-  module_path: tomopy.prep.stripe
-  parameters:
-    level: null
-    wname: db5
-    sigma: 2
-    pad: true
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml
deleted file mode 100644
index c63f6f006..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: remove_stripe_sf
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: 5
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml
deleted file mode 100644
index 3a0152b56..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: remove_stripe_ti
-  module_path: tomopy.prep.stripe
-  parameters:
-    nblock: 0
-    alpha: 1.5
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml
deleted file mode 100644
index e00632891..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: stripes_detect3d
-  module_path: tomopy.prep.stripe
-  parameters:
-    size: 10
-    radius: 3
diff --git a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml b/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml
deleted file mode 100644
index 198549b37..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-- method: stripes_mask3d
-  module_path: tomopy.prep.stripe
-  parameters:
-    weights: REQUIRED
-    threshold: 0.6
-    min_stripe_length: 20
-    min_stripe_depth: 10
-    min_stripe_width: 5
-    sensitivity_perc: 85.0
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml
deleted file mode 100644
index 8b239d362..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-- method: recon
-  module_path: tomopy.recon.algorithm
-  parameters:
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    sinogram_order: false
-    algorithm: null
-    init_recon: null
-    '#additional parameters': AVAILABLE
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.rotation/download_all.yaml
deleted file mode 100644
index c6bd656a6..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/download_all.yaml
+++ /dev/null
@@ -1,46 +0,0 @@
-- method: find_center
-  module_path: tomopy.recon.rotation
-  parameters:
-    ind: null
-    init: null
-    tol: 0.5
-    mask: true
-    ratio: 1.0
-    sinogram_order: false
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
-    overlap: overlap
-    side: side
-    overlap_position: overlap_position
-- method: write_center
-  module_path: tomopy.recon.rotation
-  parameters:
-    dpath: tmp/center
-    cen_range: null
-    ind: null
-    mask: false
-    ratio: 1.0
-    sinogram_order: false
-    algorithm: gridrec
-    filter_name: parzen
-- method: find_center_vo
-  module_path: tomopy.recon.rotation
-  parameters:
-    ind: null
-    smin: -50
-    smax: 50
-    srad: 6
-    step: 0.25
-    ratio: 0.5
-    drop: 20
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
-- method: find_center_pc
-  module_path: tomopy.recon.rotation
-  parameters:
-    proj1: REQUIRED
-    proj2: REQUIRED
-    tol: 0.5
-    rotc_guess: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml
deleted file mode 100644
index fb2b45dc7..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-- method: find_center
-  module_path: tomopy.recon.rotation
-  parameters:
-    ind: null
-    init: null
-    tol: 0.5
-    mask: true
-    ratio: 1.0
-    sinogram_order: false
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
-    overlap: overlap
-    side: side
-    overlap_position: overlap_position
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml
deleted file mode 100644
index 30961eea3..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-- method: find_center_pc
-  module_path: tomopy.recon.rotation
-  parameters:
-    proj1: REQUIRED
-    proj2: REQUIRED
-    tol: 0.5
-    rotc_guess: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml
deleted file mode 100644
index 1e213797c..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-- method: find_center_vo
-  module_path: tomopy.recon.rotation
-  parameters:
-    ind: null
-    smin: -50
-    smax: 50
-    srad: 6
-    step: 0.25
-    ratio: 0.5
-    drop: 20
-  id: centering
-  side_outputs:
-    cor: centre_of_rotation
diff --git a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/write_center.yaml b/httomo/yaml_templates/tomopy/tomopy.recon.rotation/write_center.yaml
deleted file mode 100644
index dc7b2bb5b..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.recon.rotation/write_center.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-- method: write_center
-  module_path: tomopy.recon.rotation
-  parameters:
-    dpath: tmp/center
-    cen_range: null
-    ind: null
-    mask: false
-    ratio: 1.0
-    sinogram_order: false
-    algorithm: gridrec
-    filter_name: parzen
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml
deleted file mode 100644
index 5535fdd2d..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-- method: add_drift
-  module_path: tomopy.sim.project
-  parameters:
-    amp: 0.2
-    period: 50
-    mean: 1
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml
deleted file mode 100644
index 64c99c66e..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: add_focal_spot_blur
-  module_path: tomopy.sim.project
-  parameters:
-    spotsize: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml
deleted file mode 100644
index e9b7031b8..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: add_gaussian
-  module_path: tomopy.sim.project
-  parameters:
-    mean: 0
-    std: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml
deleted file mode 100644
index 4c68479d0..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-- method: add_poisson
-  module_path: tomopy.sim.project
-  parameters: {}
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml
deleted file mode 100644
index a96c6cb8f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-- method: add_rings
-  module_path: tomopy.sim.project
-  parameters:
-    std: 0.05
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml
deleted file mode 100644
index 9777ac341..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: add_salt_pepper
-  module_path: tomopy.sim.project
-  parameters:
-    prob: 0.01
-    val: null
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml
deleted file mode 100644
index 5048a4c7e..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-- method: add_zingers
-  module_path: tomopy.sim.project
-  parameters:
-    f: 0.01
-    sat: 65536
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/download_all.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/download_all.yaml
deleted file mode 100644
index 28c48d4bd..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/download_all.yaml
+++ /dev/null
@@ -1,61 +0,0 @@
-- method: add_drift
-  module_path: tomopy.sim.project
-  parameters:
-    amp: 0.2
-    period: 50
-    mean: 1
-- method: project
-  module_path: tomopy.sim.project
-  parameters:
-    obj: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
-- method: add_poisson
-  module_path: tomopy.sim.project
-  parameters: {}
-- method: add_gaussian
-  module_path: tomopy.sim.project
-  parameters:
-    mean: 0
-    std: null
-- method: add_zingers
-  module_path: tomopy.sim.project
-  parameters:
-    f: 0.01
-    sat: 65536
-- method: add_salt_pepper
-  module_path: tomopy.sim.project
-  parameters:
-    prob: 0.01
-    val: null
-- method: project3
-  module_path: tomopy.sim.project
-  parameters:
-    objx: REQUIRED
-    objy: REQUIRED
-    objz: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
-    axis: auto
-- method: add_rings
-  module_path: tomopy.sim.project
-  parameters:
-    std: 0.05
-- method: project2
-  module_path: tomopy.sim.project
-  parameters:
-    objx: REQUIRED
-    objy: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
-    axis: auto
-- method: add_focal_spot_blur
-  module_path: tomopy.sim.project
-  parameters:
-    spotsize: REQUIRED
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/project.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/project.yaml
deleted file mode 100644
index ed843f1a5..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/project.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-- method: project
-  module_path: tomopy.sim.project
-  parameters:
-    obj: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/project2.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/project2.yaml
deleted file mode 100644
index 9b54d232f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/project2.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-- method: project2
-  module_path: tomopy.sim.project
-  parameters:
-    objx: REQUIRED
-    objy: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
-    axis: auto
diff --git a/httomo/yaml_templates/tomopy/tomopy.sim.project/project3.yaml b/httomo/yaml_templates/tomopy/tomopy.sim.project/project3.yaml
deleted file mode 100644
index c1719c87f..000000000
--- a/httomo/yaml_templates/tomopy/tomopy.sim.project/project3.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-- method: project3
-  module_path: tomopy.sim.project
-  parameters:
-    objx: REQUIRED
-    objy: REQUIRED
-    objz: REQUIRED
-    center: ${{centering.side_outputs.centre_of_rotation}}
-    emission: true
-    pad: true
-    sinogram_order: false
-    axis: auto
diff --git a/pyproject.toml b/pyproject.toml
index 5488d6353..a10e7b923 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,6 @@ httomo = [
     "methods_database/packages/external/httomolibgpu/*.yaml",
     "methods_database/packages/external/httomolib/*.yaml",
     "methods_database/packages/external/tomopy/*.yaml",
-    "yaml_templates/*/*/*.yaml",
 ]
 
 [tool.setuptools-git-versioning]
diff --git a/httomo/yaml_templates_generator.py b/scripts/yaml_templates_generator.py
similarity index 100%
rename from httomo/yaml_templates_generator.py
rename to scripts/yaml_templates_generator.py
diff --git a/httomo/yaml_unsupported_tomopy_remove.py b/scripts/yaml_unsupported_tomopy_remove.py
similarity index 100%
rename from httomo/yaml_unsupported_tomopy_remove.py
rename to scripts/yaml_unsupported_tomopy_remove.py


Test patch:
diff --git a/conda/explicit/latest.txt b/conda/explicit/latest.txt
deleted file mode 100644
index c54ac1eed..000000000
--- a/conda/explicit/latest.txt
+++ /dev/null
@@ -1,168 +0,0 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: linux-64
-@EXPLICIT
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