Edit CF-Compliance-Checker.md

It uses the [CF-Checker](https://github.com/cedadev/cf-checker) utility (`cfchecks`) and is designed for workflows where NetCDF datasets are organized in subdirectories. The script:

- Finds the **first NetCDF file** in each subdirectory of a given parent directory.  

- By default, finds the **first NetCDF file** in each subdirectory of a given parent directory.  

- With the `--all` flag, processes **all NetCDF files** in each subdirectory.  

- Runs **CF-Checker** on those files.  

- Saves results into two separate logs:

  - `cf_compliance_details.log` → detailed CF-Checker output (per file)  

  - `cf_compliance_summary.log` → summary table of results (across all files)  

- Optionally exports the summary to **CSV** or **Excel**, with timestamped filenames for reproducibility.  

- The summary table includes a **Folder** column to show the subdirectory of each file.  

---

```mermaid

flowchart TD

    A[Parent Directory] --> B[Find first NetCDF file in each subdir]

    B --> C[Run cfchecks on each file]

    C --> D[Parse CF-Checker summary (Errors, Warnings, Info)]

    D --> E[cf_compliance_details.log<br>(per-file details)]

    D --> F[cf_compliance_summary.log<br>(summary table)]

    F --> G[Optional CSV Export<br>(timestamped)]

    F --> H[Optional Excel Export<br>(timestamped)]

    A[Parent Directory] --> B[Find NetCDF files in each subdir]

    B -->|Default| C[First file only]

    B -->|--all flag| C2[All files]

    C --> D[Run cfchecks on each file]

    C2 --> D

    D --> E[Parse CF-Checker summary (Errors, Warnings, Info)]

    E --> F[cf_compliance_details.log<br>(per-file details)]

    E --> G[cf_compliance_summary.log<br>(summary table, incl. Folder column)]

    G --> H[Optional CSV Export<br>(timestamped)]

    G --> I[Optional Excel Export<br>(timestamped)]

```

---

## Usage

```bash

python check_cf_compliance.py <parent_directory> [CF_version] [--csv] [--excel]

python check_cf_compliance.py <parent_directory> [CF_version] [--all] [--csv] [--excel]

```

### Arguments

- `<parent_directory>` → Path to the parent folder containing subdirectories with NetCDF files.  

- `[CF_version]` → (Optional) CF version to check against, e.g. `1.8`.  

- `--all` → Check **all NetCDF files** in each subdirectory (default: only first file per subdir).  

- `--csv` → Export summary results to a timestamped CSV file.  

- `--excel` → Export summary results to a timestamped Excel file.  

### Examples

Check all subdirectories and just log results:

Check only the first file in each subdirectory (default):

```bash

python check_cf_compliance.py /data/netcdf_files

```

Check all files in each subdirectory:

```bash

python check_cf_compliance.py /data/netcdf_files --all

```

Check against CF-1.8:

```bash

python check_cf_compliance.py /data/netcdf_files 1.8

Export both CSV and Excel:

```bash

python check_cf_compliance.py /data/netcdf_files 1.8 --csv --excel

python check_cf_compliance.py /data/netcdf_files 1.8 --all --csv --excel

```

---

1. **Log files**

   - `cf_compliance_details.log` → detailed `cfchecks` output for each file.  

   - `cf_compliance_summary.log` → summary table with counts of Errors, Warnings, Info.  

   - `cf_compliance_summary.log` → summary table with counts of Errors, Warnings, Info, including **Folder** column.  

2. **Optional exports**

   - `cf_compliance_summary_YYYYMMDD_HHMMSS.csv` → machine-readable CSV summary.  

Example summary table in logs:

```

| File                 | Errors | Warnings | Info | Result |

|----------------------|--------|----------|------|--------|

| huragl10S1_200001.nc |      0 |        3 |    0 | PASS   |

| windagl80S1_199901.nc|      1 |        5 |    0 | FAIL   |

| Folder   | File                 | Errors | Warnings | Info | Result |

|----------|----------------------|--------|----------|------|--------|

| exp001   | huragl10S1_200001.nc |      0 |        3 |    0 | PASS   |

| exp001   | windagl80S1_199901.nc|      1 |        5 |    0 | FAIL   |

```

---

## How It Works

1. **File selection**: For each subdirectory in the parent folder, the script takes the **alphabetically first NetCDF file** (`*.nc`).  

1. **File selection**:  

   - Default: takes the **alphabetically first NetCDF file** (`*.nc`) in each subdir.  

   - With `--all`: processes **all NetCDF files** in each subdir.  

2. **Run CF-Checker**: Calls the `cfchecks` utility for each selected file.  

3. **Parse results**: Extracts the `ERRORS detected`, `WARNINGS given`, and `INFORMATION messages` lines from the CF-Checker output.  

4. **Logging**:

   - Writes all raw CF-Checker output into `cf_compliance_details.log`.  

   - Builds a concise summary table and writes it into `cf_compliance_summary.log`.  

   - Builds a concise summary table (including **Folder** column) and writes it into `cf_compliance_summary.log`.  

5. **Export** (optional): Saves the summary table into CSV/Excel with timestamped filenames for reproducibility.  

---

Future improvements could include:

- Adding `--details-only` or `--summary-only` flags to control which logs are written.  

- Processing **all files** in each subdirectory, not just the first.  

- Supporting parallel execution for large datasets.  

- Adding more granular filtering (e.g., only certain file patterns).